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Yorodumi- PDB-2rdz: High Resolution Crystal Structure of the Escherichia coli Cytochr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rdz | ||||||
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Title | High Resolution Crystal Structure of the Escherichia coli Cytochrome c Nitrite Reductase. | ||||||
Components | Cytochrome c-552 | ||||||
Keywords | OXIDOREDUCTASE / decaheme / reductase / Electron transport / Iron / Metal-binding / Transport | ||||||
Function / homology | Function and homology information nitric oxide reductase activity / nitrite reductase (cytochrome; ammonia-forming) / nitrite reductase (cytochrome, ammonia-forming) activity / anaerobic electron transport chain / nitrate assimilation / outer membrane-bounded periplasmic space / iron ion binding / calcium ion binding / heme binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.74 Å | ||||||
Authors | Clarke, T.A. / Hemmings, A.M. / RIchardson, D.J. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Role of a Conserved Glutamine Residue in Tuning the Catalytic Activity of Escherichia coli Cytochrome c Nitrite Reductase. Authors: Clarke, T.A. / Kemp, G.L. / Wonderen, J.H. / Doyle, R.M. / Cole, J.A. / Tovell, N. / Cheesman, M.R. / Butt, J.N. / Richardson, D.J. / Hemmings, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rdz.cif.gz | 432 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rdz.ent.gz | 353.5 KB | Display | PDB format |
PDBx/mmJSON format | 2rdz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2rdz_validation.pdf.gz | 7.1 MB | Display | wwPDB validaton report |
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Full document | 2rdz_full_validation.pdf.gz | 7.2 MB | Display | |
Data in XML | 2rdz_validation.xml.gz | 89.7 KB | Display | |
Data in CIF | 2rdz_validation.cif.gz | 135 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rd/2rdz ftp://data.pdbj.org/pub/pdb/validation_reports/rd/2rdz | HTTPS FTP |
-Related structure data
Related structure data | 2rf7C 1gu6S 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 50668.117 Da / Num. of mol.: 4 / Fragment: cytochrome c nitrite reductase / Source method: isolated from a natural source / Details: Periplasm / Source: (natural) Escherichia coli (E. coli) / Strain: LCB2048 References: UniProt: P0ABK9, nitrite reductase (cytochrome; ammonia-forming) |
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-Non-polymers , 5 types, 2209 molecules
#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-HEC / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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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: 2.44 Å3/Da / Density % sol: 49.58 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Crystals were obtained in 100 mM HEPES pH 7.5, 20 % PEG 10 K. , VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 18, 2004 |
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→134.84 Å / Num. all: 193642 / Num. obs: 193642 / % possible obs: 99.1 % / Redundancy: 3.9 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 1.74→1.83 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 2.1 / Num. measured all: 81691 / Num. unique all: 26673 / Rsym value: 0.351 / % possible all: 94.1 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GU6 Resolution: 1.74→39.65 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.975 / SU ML: 0.065 / Isotropic thermal model: Individual Atom Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2.8 / ESU R: 0.106 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.781 Å2
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Refinement step | Cycle: LAST / Resolution: 1.74→39.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.74→1.785 Å / Total num. of bins used: 20
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