ISSN:1399-0047    

DOI:10.1107/S0907444993011709

出版商:International Union of Crystallography    

年代:1994

数据来源: WILEY

ISSN:1399-0047    

DOI:10.1107/S0907444994099786

出版商:International Union of Crystallography    

年代:1994

数据来源: WILEY

摘要:

An essential first step in most techniques for using anomalous‐scattering data for phase determination is to determine the positions of the anomalous scatterers. This is usually done by use of the anomalous differences, either as input to a direct‐methods procedure or to produce a Patterson map. If the arrangement of anomalous scatterers is noncentrosymmetric then it is also necessary to find their absolute configuration and a process is described for doing this based on the properties of thePsfunction [Okaya, Saito&Pepinsky (1955).Phys. Rev.98, 1857–1858]. If the arrangement of anomalous scatterers is centrosymmetric then the problem does not

ISSN:1399-0047    

DOI:10.1107/S0907444993008091

出版商:International Union of Crystallography    

年代:1994

数据来源: WILEY

摘要:

A Bayesian approach is applied to the calculation of Patterson functions and cross‐Fourier maps in the analysis of multi‐wavelength anomalous‐diffraction (MAD) data. This procedure explicitly incorporates information availablea priorion the likely magnitudes of partial structure factors (FA) corresponding to the anomalously scattering atoms, uses weighted‐average estimates ofFA, and incorporates estimates of errors in the data that are not represented in the instrumental uncertainties. The method is demonstrated by application to MAD data collected on selenomethionine‐containing gene

ISSN:1399-0047    

DOI:10.1107/S0907444993008224

出版商:International Union of Crystallography    

年代:1994

数据来源: WILEY

摘要:

A framework analogous to that used for the analysis of data in the method of isomorphous replacement is applied to the analysis of multi‐wavelength anomalous‐diffraction (MAD) data. The present method is advantageous in that refinement of parameters describing the anomalously scattering atoms in the structure can be carried out using nearly all the data, and in that phase information can be readily combined. The procedure described here involves an approximation in which it is assumed that the magnitude of the structure factor corresponding to anomalously scattering atoms in the unit cell is small compared to that corresponding to all other atoms in the structure. A model calculation is applied to a protein crystal with 682 non‐H atoms in the asymmetric unit and two Se atoms as the anomalous scatterers. It is shown using this model calculation that the approximation used in this analysis does not substantially affect the accuracy of phase calculations for this MAD data. The method is demonstrated by application to MAD data collected on gene V pr

ISSN:1399-0047    

DOI:10.1107/S0907444993008236

出版商:International Union of Crystallography    

年代:1994

数据来源: WILEY

摘要:

Time‐averaged structure‐factor restraints have been used in two molecular dynamics refinement schemes to define ensembles of conformations for myoglobin that fit the experimentally measured Bragg scattering fromP6 crystals. The geometries of the structures have been maintained to the same currently acceptable limits in all cases. FreeRvalue analysis was used to assess the validity of the two approaches. In the first scheme, where atoms have noBvalues, the decrease inRvalue was found to be spurious as judged by a concomitant increase in the freeRvalue. The other scheme, however, which retains individualBvalues, was found to yield both lowRvalues and low freeRvalues; thus, here the additional variables introduced by modeling the protein in terms of an evolving ensemble of states do not overfit the data. For comparison, refinements were also carried out on the system using several other techniques for isotropic and anisotropic crystallographic refinement. The time‐averaged refinements withBvalues compare quite favorably with the standard methods, but yield additional information about substates of the system. Hence, correctly applied time‐averaged refinements can yield accurate models for protein molecules; moreover, by essentially relaxing the harmonic approximation from the refinement process, these refinements allow a more detailed description of the motions of complex molecules, such as proteins, to be determined from X‐ray crystallogra

ISSN:1399-0047    

DOI:10.1107/S0907444993009515

出版商:International Union of Crystallography    

年代:1994

数据来源: WILEY

摘要:

Pseudomonas aeruginosaazurin has been crystallized from a mutant where residues from Met 121 to Lys128 have been deleted from the protein. The crystals form pale‐blue well formed prisms in the orthorhombic space group P212121, with cell dimensionsa= 60.79 (5),b= 123.47 (5),c= 187.77 (5) Å. The crystals diffract to 3.0 Å and there are eight molecules in the as

ISSN:1399-0047    

DOI:10.1107/S0907444993008509

出版商:International Union of Crystallography    

年代:1994

数据来源: WILEY

摘要:

The structure of chicken skeletal muscle troponin C (TnC) has been refined to anRvalue of 0.168, using 14 788 reflections, in the resolution range 8.0–1.78 Å. Our earlier 2 Å resolution structure [Satyshur, Rao, Pyzalska, Drendel, Greaser&Sundaralingam (1988).J. Biol. Chem.263, 1628–1647] served as the starting model. The refined model includes atoms for all protein residues (1–162), 2 Ca2+ions, 169 water molecules and one sulfate ion. The high‐resolution refinement shows more clearly the details of the protein and water structure. The side chains Glu63, Cysl01, Arg123, Aspl40 and Asp152 adopt two discretely ordered conformations. The long central helix is only slightly curved/bent (7.9°) and all the central helix NH⋯O=C hydrogen bonds are intact. Seven of the nine carbonyl O atoms of the mid segment of this helix, including theD/Elinker region, are hydrogen bonded to water molecules which weakens the helix hydrogen bonds. In contrast, in each of the protected upper and lower thirds of the long central helix, only two carbonyl O atoms are hydrogen bonded to water molecules. The hydrogen‐bonding patterns displayed by some of the carbonyl O atoms of NT andAhelices of the N‐terminal domain and theFandHhelices of the C‐terminal domain, which are on the exposed surface of the protein, are similar. TheBhelix of the calcium‐free site I is kinked, with the local helix axes at either end making an angle of 39°, by two inserted water molecules between N—H and O=C groups, breaking the adjacent helix hydrogen bonds. A sulfate ion from the crystallization buffer is also trapped in theBhelix between the guanidinium group of Arg47 and these two inserted water molecules. TheChelix of site II is devoid of similar hydration and is probably responsible for the different interhelical anglesA/Bat site I (134°) andC/Dat site II (149°). Extensive interhelix hydrogen bonds occur between the side chains of theCandDhelices of the `apo' site II: Gln51–Asp89, Asn52–Asp89, Glu57–Gln85, Glu57–Glu88 and Glu64–Arg84, which apparently are disrupted upon Ca uptake and the resulting rearrangement of the helices expose the side chains, lining the palm of the N‐(and C‐) terminal domains, for interaction with specific peptide fragment of troponin I (Tnl) during muscle contraction. The dominant crystal packing motif involves a head‐to‐tail interaction between the N‐terminal domainAhelix of one molecule and the palm of the C‐terminal domain of the 32‐related molecule, in a manner similar to that which can be expected for the TnC–TnI complex. Similar interactions may

ISSN:1399-0047    

DOI:10.1107/S090744499300798X

出版商:International Union of Crystallography    

年代:1994

数据来源: WILEY

摘要:

The crystal structure of the recombinant calmodulin fromParamecium tetraurelia(rPCaM,Mr= 16 700, 148 residues) has been determined at 1.68 Å resolution. X‐ray intensity data were collected at 263 K using a Siemens–Nicolet area detector and CuKα radiation from a rotating‐anode source. A total of 35 936 observations were processed withXENGEN1.3 and scaled to yield 16 255 unique reflections withRsymm(I) of 4.1%. The crystals are triclinic, with unit‐cell dimensionsa= 29.89, b = 53.42,c= 25.35 Å, α = 93.67, β = 96.88, γ = 89.24°, space groupP1, with one molecule in the unit cell. The atomic coordinates of the wild‐typeParameciumcalmodulin (PCaM) studied in our laboratory provided the starting model. Refinement of the structure byX‐PLORand refitting it into omit maps yielded anRvalue of 0.194 for 15 965 reflections greater than 3σ(F) in the 6.0–1.68 Å resolution range. The final model contained 1165 protein atoms for all of the 148 residues, four Ca2+ions, and 172 water molecules. The dumbbell structure has seven α‐helices including a long 7.8 turn central helix connecting the two terminal domains each containing twoEF‐hand (helix–loop–helix motif) calcium‐binding sites. The loops within each pair ofEF‐hand motifs in the N‐ and C‐terminal domains are brought into juxtaposition to form a pair of hydrogen‐bonded antiparallel β‐sheets which are extended at either ends by water bridges. The four calcium‐bindingEF‐hands are superposable with r.m.s. deviations of 0.31–0.79 Å. The best agreement is between site 1 and site 3 and the worst agreement is between site 1 and 4. The largest differences are in the ninth and tenth residues of the calcium‐binding loops probably because of their involvement in the mini β‐sheets. The calcium coordination distances vary between 2.04 and 2.69 Å, average 2.34 Å. The rPCaM and wild‐type PCaM have an r.m.s. deviation of 0.36 Å for equivalent Cαatoms. The side chains of Lys13 and Lys115 are more extended in rPCaM compared to the wild type where the post‐translational modified di‐ and tri‐methylated lysine residues are more folded. The sequence of PCaM differs from those of mammalian (MCaM) andDrosophilacalmodulin (DCaM), but the overall structures are very similar, with r.m.s,. deviations of 0.44 and 1.68 Å for equivalent Cαatoms, respectively. However, in rPCaM, the first four N‐terminal residues stretch out and make intermolecular crystal contacts, in contrast to those in recombinantDrosophilacalmodulin (rDCaM), they stretch out in the opposite direction and towards the second calcium‐binding site (see note below), while in MCaM and wild‐type PCaM, the N‐terminal residues are not visible. The central helix in rPCaM has all its backbone hydrogen bonds i

ISSN:1399-0047    

DOI:10.1107/S0907444993007991

出版商:International Union of Crystallography    

年代:1994

数据来源: WILEY

摘要:

The mouse monoclonal antibodies (mAb), 2E5.G10 and 1F5.D1, are specific for horse cytochromecand appear to bind the same epitope, since their heavy (H) and light (L) chains are functionally interchangeable. Comparison of the amino‐acid sequences suggests that slightly different interactions may be involved in antigen recognition. In addition, the H chains differ at only a few amino‐acid residues from the H chain of a rat cytochromec‐specific mAb suggesting that specificity for one protein over another may be determined by these amino‐acid differences. To address these possibilities, the three‐dimensional structures of the Fab portions of the mAb bound to cytochromecare being determined by X‐ray diffraction analysis. Here we describe the preparation and crystallization of the two complexes with horse cytochromec. The complex of the Fab fragment of 2E5.G10 with horse cytochromecyielded crystals of X‐ray diffraction quality under two sets of conditions; in both the space group wasP21. The corresponding complex of 1F5.D1 under one of these conditions crystallized in theP212121space group. Three‐dimensional X‐ray data for these two complexes have been collected with nominal resolutions of 2.86 and 2.4

ISSN:1399-0047    

DOI:10.1107/S0907444993009084

出版商:International Union of Crystallography    

年代:1994

数据来源: WILEY