+Open data
-Basic information
Entry | Database: PDB / ID: 1.0E+61 | ||||||
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Title | OXIDIZED DMSO REDUCTASE EXPOSED TO HEPES - Structure II BUFFER | ||||||
Components | Dimethyl sulfoxide/trimethylamine N-oxide reductase | ||||||
Keywords | OXIDOREDUCTASE / REDUCTASE / DMSO / MOLYBDOPTERIN | ||||||
Function / homology | Function and homology information trimethylamine-N-oxide reductase activity / respiratory dimethylsulfoxide reductase / trimethylamine-N-oxide reductase / trimethylamine-N-oxide reductase (cytochrome c) activity / molybdopterin cofactor binding / periplasmic space / metal ion binding Similarity search - Function | ||||||
Biological species | Rhodobacter capsulatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Bailey, S. / Bennett, B. / Adams, B. / Smith, A.T. / Bray, R.C. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Reversible Dissociation of Thiolate Ligands from Molybdenum in an Enzyme of the Dimethyl Sulfoxide Reductase Family Authors: Bray, R.C. / Adams, B. / Smith, A.T. / Bennett, B. / Bailey, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e61.cif.gz | 325.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e61.ent.gz | 258.6 KB | Display | PDB format |
PDBx/mmJSON format | 1e61.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/1e61 ftp://data.pdbj.org/pub/pdb/validation_reports/e6/1e61 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.03048, -0.07809, -0.99648), Vector: |
-Components
#1: Protein | Mass: 89525.938 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus (bacteria) / Cellular location: PERIPLASM References: UniProt: Q52675, trimethylamine-N-oxide reductase, respiratory dimethylsulfoxide reductase #2: Chemical | ChemComp-PGD / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Compound details | REDUCES VARIOUS N-OXIDE AND SULFOXIDE COMPOUNDS INCLUDING TRIMETHYLAMINE N-OXIDE DURING ANAEROBIC ...REDUCES VARIOUS N-OXIDE AND SULFOXIDE COMPOUNDS INCLUDING TRIMETHYLA | |
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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: 2.76 Å3/Da / Density % sol: 45 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: 0.1M HEPES BUFFER, PH 7.5 - 2M AMMONIUM SULPHATE 3-4% PEG 400 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20-22 ℃ / pH: 7 / Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 15, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 121768 / % possible obs: 78.2 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 1.9→1.91 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 2.8 / % possible all: 52.9 |
Reflection | *PLUS Num. measured all: 367035 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: DMSO REDUCTASE FROM RHODOBACTER CAPSULATUS Resolution: 1.9→20 Å / SU B: 3.2 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.15
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å / Rfactor obs: 0.178 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |