+Open data
-Basic information
Entry | Database: PDB / ID: 1tmo | ||||||
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Title | TRIMETHYLAMINE N-OXIDE REDUCTASE FROM SHEWANELLA MASSILIA | ||||||
Components | TRIMETHYLAMINE N-OXIDE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / TMAO REDUCTASE / OXOTRANSFERASE / MOLYBDOENZYME / MO-COFACTOR / MOLYBDENUM / BIS (MOLYBDOPTERIN GUANINE DINUCLEOTIDE) | ||||||
Function / homology | Function and homology information trimethylamine-N-oxide reductase / trimethylamine-N-oxide reductase (cytochrome c) activity / molybdenum ion binding / molybdopterin cofactor binding / periplasmic space Similarity search - Function | ||||||
Biological species | Shewanella massilia (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å | ||||||
Authors | Czjzek, M. / Dos Santos, J.P. / Giordano, G. / Mejean, V. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: Crystal structure of oxidized trimethylamine N-oxide reductase from Shewanella massilia at 2.5 A resolution. Authors: Czjzek, M. / Dos Santos, J.P. / Pommier, J. / Giordano, G. / Mejean, V. / Haser, R. #1: Journal: J.Mol.Biol. / Year: 1998 Title: Molecular Analysis of the Trimethylamine N-Oxide (Tmao) Reductase Respiratory System from a Shewanella Species Authors: Dos Santos, J.P. / Iobbi-Nivol, C. / Couillault, C. / Giordano, G. / Mejean, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tmo.cif.gz | 182.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tmo.ent.gz | 140.7 KB | Display | PDB format |
PDBx/mmJSON format | 1tmo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tmo_validation.pdf.gz | 963.5 KB | Display | wwPDB validaton report |
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Full document | 1tmo_full_validation.pdf.gz | 974.6 KB | Display | |
Data in XML | 1tmo_validation.xml.gz | 34.6 KB | Display | |
Data in CIF | 1tmo_validation.cif.gz | 51.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tm/1tmo ftp://data.pdbj.org/pub/pdb/validation_reports/tm/1tmo | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 92476.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: MARINE BACTERIA, ISOLATED FROM THE FISH MULLUS SURMULETUS Source: (natural) Shewanella massilia (bacteria) / Cellular location: PERIPLASM / References: UniProt: O87948, EC: 1.6.6.9 | ||||
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#2: Chemical | #3: Chemical | ChemComp-2MO / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 64 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
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: EMBL/DESY, HAMBURG / Beamline: X31 |
Detector | Date: Dec 1, 1997 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Biso Wilson estimate: 15.2 Å2 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 25 Å / Num. obs: 37497 / % possible obs: 92 % / Rmerge(I) obs: 0.14 |
Reflection shell | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 2.61 Å / % possible obs: 81 % / Num. unique obs: 4403 / Rmerge(I) obs: 0.48 |
-Processing
Software |
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Refinement | Resolution: 2.5→20 Å / Data cutoff high absF: 10000000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.5 Details: TWO REFINEMENTS WERE DONE IN PARALLEL: ONE WITH TEST-SET AND ONE WITHOUT. THE FINAL, GLOBAL R-FACTOR GIVEN INCLUDES ALL REFLECTIONS AND NOT ONLY THOSE OF THE WORKING SET.
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Displacement parameters | Biso mean: 13.31 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.27 Å / Luzzati d res low obs: 3 Å / Luzzati sigma a obs: 0.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.61 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.225 |