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Yorodumi- PDB-2c3c: 2.01 Angstrom X-ray crystal structure of a mixed disulfide betwee... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c3c | ||||||
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Title | 2.01 Angstrom X-ray crystal structure of a mixed disulfide between coenzyme M and NADPH-dependent oxidoreductase 2-ketopropyl coenzyme M carboxylase | ||||||
Components | 2-OXOPROPYL-COM REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / MIXED DISULFIDE / COENZYME M / REDOX-ACTIVE CENTER / FAD | ||||||
Function / homology | Function and homology information 2-oxopropyl-CoM reductase (carboxylating) / 2-oxopropyl-CoM reductase (carboxylating) activity / propylene catabolic process / flavin adenine dinucleotide binding Similarity search - Function | ||||||
Biological species | XANTHOBACTER AUTOTROPHICUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Pandey, A.S. / Nocek, B. / Clark, D.D. / Ensign, S.A. / Peters, J.W. | ||||||
Citation | Journal: Biochemistry / Year: 2006 Title: Mechanistic Implications of the Structure of the Mixed-Disulfide Intermediate of the Disulfide Oxidoreductase, 2-Ketopropyl-Coenzyme M Oxidoreductase/Carboxylase. Authors: Pandey, A.S. / Nocek, B. / Clark, D.D. / Ensign, S.A. / Peters, J.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2c3c.cif.gz | 231.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c3c.ent.gz | 184.2 KB | Display | PDB format |
PDBx/mmJSON format | 2c3c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/2c3c ftp://data.pdbj.org/pub/pdb/validation_reports/c3/2c3c | HTTPS FTP |
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-Related structure data
Related structure data | 2c3dC 1mo9S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 57414.348 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) XANTHOBACTER AUTOTROPHICUS (bacteria) / Strain: PY2 References: UniProt: Q56839, 2-oxopropyl-CoM reductase (carboxylating) |
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-Non-polymers , 5 types, 719 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | CATALYZES THE REDUCTIVE CLEAVAGE OF THE THIOETHER LINKAGE OF 2-KETOPROPYL-COENZYME M, AND THE ...CATALYZES THE REDUCTIVE CLEAVAGE OF THE THIOETHER LINKAGE OF 2-KETOPROPYL |
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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: 2.6 Å3/Da / Density % sol: 52.6 % |
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Crystal grow | pH: 4.5 Details: 0.1 M AMMONIUM ACETATE 0.085M SODIUM CITRATE PH 5.6 25% PEG4000 30% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 1, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→20 Å / Num. obs: 62300 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.04→2.09 Å / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.5 / % possible all: 82.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MO9 Resolution: 2.15→36.99 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1415780.28 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.2051 Å2 / ksol: 0.372272 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.15→36.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.28 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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