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Yorodumi- PDB-2je2: Cytochrome P460 from Nitrosomonas europaea - probable nonphysiolo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2je2 | ||||||
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Title | Cytochrome P460 from Nitrosomonas europaea - probable nonphysiological oxidized form | ||||||
Components | CYTOCHROME P460 | ||||||
Keywords | METAL BINDING PROTEIN / HEME P460 / CYTOCHROME P460 / CROSS-LINKED HEME | ||||||
Function / homology | Function and homology information | ||||||
Biological species | NITROSOMONAS EUROPAEA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Pearson, A.R. / Elmore, B.O. / Yang, C. / Ferrara, J.D. / Hooper, A.B. / Wilmot, C.M. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: The Crystal Structure of Cytochrome P460 of Nitrosomonas Europaea Reveals a Novel Cytochrome Fold and Heme-Protein Cross-Link. Authors: Pearson, A.R. / Elmore, B.O. / Yang, C. / Ferrara, J.D. / Hooper, A.B. / Wilmot, C.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2je2.cif.gz | 50.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2je2.ent.gz | 35.2 KB | Display | PDB format |
PDBx/mmJSON format | 2je2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2je2_validation.pdf.gz | 881.1 KB | Display | wwPDB validaton report |
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Full document | 2je2_full_validation.pdf.gz | 884.6 KB | Display | |
Data in XML | 2je2_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 2je2_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/je/2je2 ftp://data.pdbj.org/pub/pdb/validation_reports/je/2je2 | HTTPS FTP |
-Related 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: 20528.113 Da / Num. of mol.: 1 / Fragment: RESIDUES 27-198 Source method: isolated from a genetically manipulated source Details: PROTEIN-HEME CROSS-LINK FROM NZ OF LYS 70 TO CHA OF HEC 200. PROTEIN-HEME CROSSLINK FROM SG OF CYS 136 TO CAB OF HEC 200. PROTEIN-HEME CROSSLINK FROM SG OF CYS 139 TO CAC OF HEC 200. Source: (gene. exp.) NITROSOMONAS EUROPAEA (bacteria) Description: CONTAINS ADDITIONAL N-TERMINAL METHIONINE AND AT THE TERMINUS THE ADDITIONS RESIDUES KLAAALEHHHHHH Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q50927 | ||||
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#2: Chemical | ChemComp-HEC / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | RECOMBINAN | |
-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: 51.1 % Description: THE STRUCTURE WAS SOLVED BY SAD USING A DATASET COLLECTED AT CR K-ALPHA. PHASED USING SHELX AND SHARP. THE INITIAL MODEL WAS THEN USED TO PHASE THE HIGHER RESOLUTION CU K-ALPHA DATASET. |
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Crystal grow | pH: 5.2 / Details: pH 5.20 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: May 5, 2005 / Details: VARIMAX CONFOCAL MAXFLUX |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→43 Å / Num. obs: 17631 / % possible obs: 80.9 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Biso Wilson estimate: 25.3 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.69→1.75 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 2.8 / % possible all: 13.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: INITIAL MODEL FROM SULPHUR SAD STRUCTURE Resolution: 1.8→43.36 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.127 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.3 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→43.36 Å
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Refine LS restraints |
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