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Yorodumi- PDB-3vcr: Crystal structure of a putative Kdpg (2-keto-3-deoxy-6-phosphoglu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vcr | ||||||||||||
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Title | Crystal structure of a putative Kdpg (2-keto-3-deoxy-6-phosphogluconate) aldolase from Oleispira antarctica | ||||||||||||
Components | putative Kdpg (2-keto-3-deoxy-6-phosphogluconate) aldolase | ||||||||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / ALDOLASE SUPERFAMILY / CLASS I ALDOLASE / KDPG ALDOLASE DOMAIN / ALPHA/BETA PROTEIN / TIM BETA/ALPHA BARREL / TIM BARREL / PSI-2 / PROTEIN STRUCTURE INITIATIVE / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG | ||||||||||||
Function / homology | Function and homology information 2-dehydro-3-deoxy-phosphogluconate aldolase / 2-dehydro-3-deoxy-phosphogluconate aldolase activity Similarity search - Function | ||||||||||||
Biological species | Oleispira antarctica (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.84 Å | ||||||||||||
Authors | Stogios, P.J. / Kagan, O. / Di Leo, R. / Yim, V. / Joachimiak, A. / Edwards, A.M. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG) | ||||||||||||
Citation | Journal: Nat Commun / Year: 2013 Title: Genome sequence and functional genomic analysis of the oil-degrading bacterium Oleispira antarctica. Authors: Kube, M. / Chernikova, T.N. / Al-Ramahi, Y. / Beloqui, A. / Lopez-Cortez, N. / Guazzaroni, M.E. / Heipieper, H.J. / Klages, S. / Kotsyurbenko, O.R. / Langer, I. / Nechitaylo, T.Y. / ...Authors: Kube, M. / Chernikova, T.N. / Al-Ramahi, Y. / Beloqui, A. / Lopez-Cortez, N. / Guazzaroni, M.E. / Heipieper, H.J. / Klages, S. / Kotsyurbenko, O.R. / Langer, I. / Nechitaylo, T.Y. / Lunsdorf, H. / Fernandez, M. / Juarez, S. / Ciordia, S. / Singer, A. / Kagan, O. / Egorova, O. / Alain Petit, P. / Stogios, P. / Kim, Y. / Tchigvintsev, A. / Flick, R. / Denaro, R. / Genovese, M. / Albar, J.P. / Reva, O.N. / Martinez-Gomariz, M. / Tran, H. / Ferrer, M. / Savchenko, A. / Yakunin, A.F. / Yakimov, M.M. / Golyshina, O.V. / Reinhardt, R. / Golyshin, P.N. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vcr.cif.gz | 145.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vcr.ent.gz | 110.1 KB | Display | PDB format |
PDBx/mmJSON format | 3vcr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vc/3vcr ftp://data.pdbj.org/pub/pdb/validation_reports/vc/3vcr | HTTPS FTP |
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-Related structure data
Related structure data | 3i4qC 3iruC 3lmbC 3lnpC 3m16C 3qvmC 3v77C 1wbhS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 22950.146 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oleispira antarctica (bacteria) / Plasmid: P15TV-L / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D2YW47 #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: 2.92 Å3/Da / Density % sol: 57.89 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 20% PEG 4000, 10% 2-PROPANOL, 0.1M TRI-SODIUM CITRATE PH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Sep 22, 2009 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. obs: 44282 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Redundancy: 4.91 % / Rsym value: 0.063 / Net I/σ(I): 27.29 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 4.45 / Rsym value: 0.115 / % possible all: 85.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WBH Resolution: 1.84→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 7.361 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.123 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.5 Å2
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Refinement step | Cycle: LAST / Resolution: 1.84→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.839→1.887 Å / Total num. of bins used: 20
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Refinement TLS params. | L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: -0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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