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Yorodumi- PDB-2ola: Crystal structure of O-succinylbenzoic acid synthetase from Staph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ola | ||||||
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Title | Crystal structure of O-succinylbenzoic acid synthetase from Staphylococcus aureus, cubic crystal form | ||||||
Components | O-succinylbenzoic acid synthetase | ||||||
Keywords | LIGASE / 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 | Function and homology information O-succinylbenzoate synthase activity / o-succinylbenzoate synthase / menaquinone biosynthetic process / magnesium ion binding Similarity search - Function | ||||||
Biological species | Staphylococcus aureus subsp. aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Patskovsky, Y. / Sauder, J.M. / Ozyurt, S. / Wasserman, S.R. / Smith, D. / Dickey, M. / Maletic, M. / Reyes, C. / Gheyi, T. / Gerlt, J.A. ...Patskovsky, Y. / Sauder, J.M. / Ozyurt, S. / Wasserman, S.R. / Smith, D. / Dickey, M. / Maletic, M. / Reyes, C. / Gheyi, T. / Gerlt, J.A. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ola.cif.gz | 83 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ola.ent.gz | 62.9 KB | Display | PDB format |
PDBx/mmJSON format | 2ola.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ola_validation.pdf.gz | 430.7 KB | Display | wwPDB validaton report |
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Full document | 2ola_full_validation.pdf.gz | 434.3 KB | Display | |
Data in XML | 2ola_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 2ola_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ol/2ola ftp://data.pdbj.org/pub/pdb/validation_reports/ol/2ola | HTTPS FTP |
-Related structure data
Related structure data | 1wueSC 1wufC 2oktC 2oztC 2pgeC 3cawC 3h70C 3h7vC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Staphylococcus aureus subsp. aureus (bacteria) Species: Staphylococcus aureus / Strain: COL / Gene: menc / Plasmid: BC-pSGX3(BC) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q53635, UniProt: A0A0H3KH80*PLUS, o-succinylbenzoate-CoA ligase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.1 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.8M Sodium malonate, PH 7.0, 10% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9794 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 3, 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: 2.45→50 Å / Num. all: 18662 / Num. obs: 18662 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 22.6 % / Biso Wilson estimate: 76 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.055 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.45→2.54 Å / Redundancy: 22.9 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 3 / Num. unique all: 1841 / Rsym value: 0.47 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1WUE Resolution: 2.45→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / SU B: 10.375 / SU ML: 0.231 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.338 / ESU R Free: 0.256 / 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: 69.584 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.51 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 20
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