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Yorodumi- PDB-2x2o: The flavoprotein NrdI from Bacillus cereus with the initially oxi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x2o | ||||||
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Title | The flavoprotein NrdI from Bacillus cereus with the initially oxidized FMN cofactor in an intermediate radiation reduced state | ||||||
Components | NRDI PROTEIN | ||||||
Keywords | FLAVOPROTEIN / RIBONUCLEOTIDE REDUCTASE / FLAVODOXIN / ELECTRON TRANSFER | ||||||
Function / homology | Function and homology information | ||||||
Biological species | BACILLUS CEREUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 Å | ||||||
Authors | Rohr, A.K. / Hersleth, H.P. / Andersson, K.K. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2010 Title: Tracking Flavin Conformations in Protein Crystal Structures with Raman Spectroscopy and Qm/Mm Calculations Authors: Rohr, A.K. / Hersleth, H.P. / Andersson, K.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x2o.cif.gz | 73.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x2o.ent.gz | 52.5 KB | Display | PDB format |
PDBx/mmJSON format | 2x2o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2x2o_validation.pdf.gz | 748.8 KB | Display | wwPDB validaton report |
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Full document | 2x2o_full_validation.pdf.gz | 750.7 KB | Display | |
Data in XML | 2x2o_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 2x2o_validation.cif.gz | 12.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x2/2x2o ftp://data.pdbj.org/pub/pdb/validation_reports/x2/2x2o | HTTPS FTP |
-Related structure data
Related structure data | 2x2pC 1rljS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13539.261 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS CEREUS (bacteria) / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q81G57 | ||||
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#2: Chemical | ChemComp-FMN / | ||||
#3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-CAC / | #5: 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: 2.05 Å3/Da / Density % sol: 40.14 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 0.1 M SODIUM CACODYLATE TRIHYDRATE PH 6.5, 0.2 M ZINC ACETATE DIHYDRATE, 14 %(W/V) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.7092 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 6, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7092 Å / Relative weight: 1 |
Reflection | Resolution: 1.13→34.2 Å / Num. obs: 42556 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.13→1.19 Å / Redundancy: 4 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RLJ Resolution: 1.13→30 Å / Num. parameters: 10677 / Num. restraintsaints: 13237 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: THE FLAVIN COFACTOR IS IN AN INTERMEDIATE ONE ELECTRON STATE.
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 9 / Occupancy sum hydrogen: 920 / Occupancy sum non hydrogen: 1131.18 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.13→30 Å
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Refine LS restraints |
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