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Yorodumi- PDB-3caw: Crystal structure of o-succinylbenzoate synthase from Bdellovibri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3caw | ||||||
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Title | Crystal structure of o-succinylbenzoate synthase from Bdellovibrio bacteriovorus liganded with Mg | ||||||
Components | o-succinylbenzoate synthase | ||||||
Keywords | OXIDOREDUCTASE / Structural Genomics / PSI-2 / NYSGXRC / target 9462a / o-Succinylbenzoate Synthase / Protein Structure Initiative / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bdellovibrio bacteriovorus HD100 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.87 Å | ||||||
Authors | Fedorov, A.A. / Fedorov, E.V. / Sakai, A. / Burley, S.K. / Gerlt, J.A. / Almo, S.C. / 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 | 3caw.cif.gz | 139 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3caw.ent.gz | 109.9 KB | Display | PDB format |
PDBx/mmJSON format | 3caw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ca/3caw ftp://data.pdbj.org/pub/pdb/validation_reports/ca/3caw | HTTPS FTP |
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-Related structure data
Related structure data | 1wueC 1wufC 2oktC 2olaC 2oztC 2pgeC 3h70C 3h7vC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 37451.234 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bdellovibrio bacteriovorus HD100 (bacteria) Species: Bdellovibrio bacteriovorus / Strain: HD100 / DSM 50701 / NCIB 9529 / Gene: Bd0547 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6MQC7 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 22% PEG 3350, 0.1M Hepes, 0.2M Magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 3, 2008 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→25 Å / Num. all: 52136 / Num. obs: 52136 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.069 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.87→24.85 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1512103.08 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.6233 Å2 / ksol: 0.387601 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.87→24.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.87→1.94 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 10
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Xplor file |
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