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- PDB-2okt: Crystal structure of O-succinylbenzoic acid synthetase from Staph... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2okt | ||||||
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Title | Crystal structure of O-succinylbenzoic acid synthetase from Staphylococcus aureus, ligand-free form | ||||||
![]() | O-succinylbenzoic acid synthetase | ||||||
![]() | LYASE / ENOLASE / O-SUCCINYLBENZOIC ACID SYNTHETASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / PSI / NYSGRC / NEW YORK STRUCTURAL GENOMICS RESEARCH CONSORTIUM / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | ![]() o-succinylbenzoate synthase / O-succinylbenzoate synthase activity / menaquinone biosynthetic process / magnesium ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Patskovsky, Y. / Toro, R. / Malashkevich, V. / Sauder, J.M. / Ozyurt, S. / Smith, D. / Dickey, M. / Maletic, M. / Powell, A. / Gheyi, T. ...Patskovsky, Y. / Toro, R. / Malashkevich, V. / Sauder, J.M. / Ozyurt, S. / Smith, D. / Dickey, M. / Maletic, M. / Powell, A. / Gheyi, T. / Wasserman, S.R. / Gerlt, J. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
![]() | ![]() Title: Loss of quaternary structure is associated with rapid sequence divergence in the OSBS family. Authors: Odokonyero, D. / Sakai, A. / Patskovsky, Y. / Malashkevich, V.N. / Fedorov, A.A. / Bonanno, J.B. / Fedorov, E.V. / Toro, R. / Agarwal, R. / Wang, C. / Ozerova, N.D. / Yew, W.S. / Sauder, J.M. ...Authors: Odokonyero, D. / Sakai, A. / Patskovsky, Y. / Malashkevich, V.N. / Fedorov, A.A. / Bonanno, J.B. / Fedorov, E.V. / Toro, R. / Agarwal, R. / Wang, C. / Ozerova, N.D. / Yew, W.S. / Sauder, J.M. / Swaminathan, S. / Burley, S.K. / Almo, S.C. / Glasner, M.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 184.4 KB | Display | ![]() |
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PDB format | ![]() | 146.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 423.7 KB | Display | ![]() |
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Full document | ![]() | 426.1 KB | Display | |
Data in XML | ![]() | 20.6 KB | Display | |
Data in CIF | ![]() | 32.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1wueSC ![]() 1wufC ![]() 2olaC ![]() 2oztC ![]() 2pgeC ![]() 3cawC ![]() 3h70C ![]() 3h7vC S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 39095.566 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Species: Staphylococcus aureus / Strain: COL / Gene: menc / Plasmid: BC-pSGX3(BC) / Species (production host): Escherichia coli / Production host: ![]() ![]() References: UniProt: Q53635, UniProt: A0A0H2WWB5*PLUS, o-succinylbenzoate synthase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 44 % |
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Crystal grow | Temperature: 294 K / pH: 8.5 Details: O.1M TRIS-HCL, PH 8.5, 30% PEG 4000, 0.2M SODIUM ACETATE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, temperature 294K, pH 8.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 6, 2006 / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→50 Å / Num. obs: 84257 / % possible obs: 99.5 % / Observed criterion σ(I): -1 / Redundancy: 3.7 % / Biso Wilson estimate: 15.69 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.032 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 1.3→1.35 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.4 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1WUE Resolution: 1.3→20 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.731 / SU ML: 0.033 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.21 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.33 Å / Total num. of bins used: 20
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