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Yorodumi- PDB-2vrc: Crystal structure of the Citrobacter sp. triphenylmethane reducta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vrc | ||||||
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Title | Crystal structure of the Citrobacter sp. triphenylmethane reductase complexed with NADP(H) | ||||||
Components | (TRIPHENYLMETHANE REDUCTASE) x 2 | ||||||
Keywords | OXIDOREDUCTASE / REDUCTASE / SDR FAMILY / TRIPHENYLMETHANE REDUCTION | ||||||
Function / homology | Function and homology information | ||||||
Biological species | CITROBACTER SP. MY-5 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | ||||||
Authors | Kim, Y. / Park, H.J. / Kwak, S.N. / Lee, J.S. / Oh, T.K. / Kim, M.H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Structural Insight Into Bioremediation of Triphenylmethane Dyes by Citrobacter Sp. Triphenylmethane Reductase. Authors: Kim, M.H. / Kim, Y. / Park, H.J. / Lee, J.S. / Kwak, S.N. / Jung, W.H. / Lee, S.G. / Kim, D. / Lee, Y.C. / Oh, T.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vrc.cif.gz | 219.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vrc.ent.gz | 184.3 KB | Display | PDB format |
PDBx/mmJSON format | 2vrc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vr/2vrc ftp://data.pdbj.org/pub/pdb/validation_reports/vr/2vrc | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31051.574 Da / Num. of mol.: 3 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) CITROBACTER SP. MY-5 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSSETA GAMI (DE3) / References: UniProt: Q2TNI4 #2: Protein | | Mass: 31039.520 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) CITROBACTER SP. MY-5 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSSETA GAMI (DE3) / References: UniProt: Q2TNI4 #3: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, LEU 21 TO MSE ENGINEERED RESIDUE IN CHAIN A, LYS 22 TO ALA ...ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61 % / Description: NONE |
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Crystal grow | pH: 8 Details: 0.3M NAH2PO4,1.2M KH2PO4,0.2M NACL, 0.1M IMIDAZOLE(PH 8.0) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 0.97947 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97947 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 56316 / % possible obs: 100 % / Observed criterion σ(I): -2 / Redundancy: 6.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 42.2 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 6 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 8.45 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.5→29.36 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.917 / SU B: 16.174 / SU ML: 0.183 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.365 / ESU R Free: 0.254 / 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: 41.55 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→29.36 Å
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Refine LS restraints |
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