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Yorodumi- PDB-5exd: Crystal structure of oxalate oxidoreductase from Moorella thermoa... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5exd | ||||||
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Title | Crystal structure of oxalate oxidoreductase from Moorella thermoacetica bound with carboxy-di-oxido-methyl-TPP (COOM-TPP) intermediate | ||||||
Components | (Oxalate oxidoreductase subunit ...) x 3 | ||||||
Keywords | OXIDOREDUCTASE / oxalate / OFOR / thiamine | ||||||
Function / homology | Function and homology information oxalate oxidoreductase / oxidoreductase activity, acting on the aldehyde or oxo group of donors, iron-sulfur protein as acceptor / oxalate catabolic process / thiamine pyrophosphate binding / 4 iron, 4 sulfur cluster binding / metal ion binding Similarity search - Function | ||||||
Biological species | Moorella thermoacetica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Gibson, M.I. / Chen, P.Y.-T. / Drennan, C.L. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: One-carbon chemistry of oxalate oxidoreductase captured by X-ray crystallography. Authors: Gibson, M.I. / Chen, P.Y. / Johnson, A.C. / Pierce, E. / Can, M. / Ragsdale, S.W. / Drennan, C.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5exd.cif.gz | 753.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5exd.ent.gz | 607.9 KB | Display | PDB format |
PDBx/mmJSON format | 5exd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ex/5exd ftp://data.pdbj.org/pub/pdb/validation_reports/ex/5exd | HTTPS FTP |
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-Related structure data
Related structure data | 5exeC 5c4iS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Oxalate oxidoreductase subunit ... , 3 types, 12 molecules ADGJBEHKCFIL
#1: Protein | Mass: 43737.645 Da / Num. of mol.: 4 / Source method: isolated from a natural source Source: (natural) Moorella thermoacetica (strain ATCC 39073) (bacteria) Strain: ATCC 39073 / References: UniProt: Q2RI41, oxalate oxidoreductase #2: Protein | Mass: 33960.750 Da / Num. of mol.: 4 / Source method: isolated from a natural source Source: (natural) Moorella thermoacetica (strain ATCC 39073) (bacteria) Strain: ATCC 39073 / References: UniProt: Q2RI40, oxalate oxidoreductase #3: Protein | Mass: 34277.535 Da / Num. of mol.: 4 / Source method: isolated from a natural source Source: (natural) Moorella thermoacetica (strain ATCC 39073) (bacteria) Strain: ATCC 39073 / References: UniProt: Q2RI42, oxalate oxidoreductase |
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-Non-polymers , 5 types, 37 molecules
#4: Chemical | ChemComp-SF4 / #5: Chemical | #6: Chemical | ChemComp-MG / #7: Chemical | ChemComp-O2T / [ | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.02 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Crystals were grown in a Coy anaerobic chamber under an Ar/H2 gas mixture. OOR was mixed with the well solution containing PEG 3000 and Tacsimate (pH 7.0). |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 2, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection twin | Operator: h,-k,-l / Fraction: 0.64 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 131808 / % possible obs: 93.2 % / Redundancy: 4.7 % / Rsym value: 0.183 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.641 / Mean I/σ(I) obs: 1.9 / % possible all: 64.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5C4I Resolution: 2.5→48.942 Å / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 32.91 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→48.942 Å
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Refine LS restraints |
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LS refinement shell |
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