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Yorodumi- PDB-1ehe: CRYSTAL STRUCTURES OF CYTOCHROME P450NOR AND ITS MUTANTS (SER286 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ehe | ||||||
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Title | CRYSTAL STRUCTURES OF CYTOCHROME P450NOR AND ITS MUTANTS (SER286 VAL, THR) IN THE FERRIC RESTING STATE AT CRYOGENIC TEMPERATURE: A COMPARATIVE ANALYSIS WITH MONOOXYGENASE CYTOCHROME P450S | ||||||
Components | CYTOCHROME P450NOR | ||||||
Keywords | OXIDOREDUCTASE / nitric oxide reductase / Cytochrome P450nor | ||||||
Function / homology | Function and homology information nitric oxide reductase [NAD(P)+, nitrous oxide-forming] / nitric oxide reductase (NAD(P)H) activity / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Fusarium oxysporum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å | ||||||
Authors | Shimizu, H. / Park, S. | ||||||
Citation | Journal: J.Inorg.Biochem. / Year: 2000 Title: Crystal structures of cytochrome P450nor and its mutants (Ser286-->Val, Thr) in the ferric resting state at cryogenic temperature: a comparative analysis with monooxygenase cytochrome P450s. Authors: Shimizu, H. / Park, S. / Lee, D. / Shoun, H. / Shiro, Y. #1: Journal: Nat.Struct.Biol. / Year: 1997 Title: Crystal structure of nitric oxide reductase from denitrifying fungus Fusarium oxysporum Authors: Park, S. / Shimizu, H. / Adachi, S. / Nakagawa, A. / Tanaka, I. / Nakahara, K. / Shoun, H. / Obayashi, E. / Nakamura, H. / Iizuka, T. / Shiro, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ehe.cif.gz | 97.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ehe.ent.gz | 72.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ehe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ehe_validation.pdf.gz | 463.7 KB | Display | wwPDB validaton report |
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Full document | 1ehe_full_validation.pdf.gz | 465.8 KB | Display | |
Data in XML | 1ehe_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | 1ehe_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eh/1ehe ftp://data.pdbj.org/pub/pdb/validation_reports/eh/1ehe | 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: 44420.691 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fusarium oxysporum (fungus) / Plasmid: PRSET-C / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 / References: UniProt: P23295, nitric-oxide reductase |
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#2: Chemical | ChemComp-HEM / |
#3: 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: 2.15 Å3/Da / Density % sol: 42.78 % | |||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: protein was crystallized from 100mM-Mes buffer, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.2 | |||||||||||||||||||||||||||||||||||||||||||||
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: SPring-8 / Beamline: BL44B2 / Wavelength: 0.7 |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jun 6, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→100 Å / Num. all: 239423 / Num. obs: 41485 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.339 / Num. unique all: 3654 / % possible all: 86.5 |
Reflection shell | *PLUS % possible obs: 86.5 % |
-Processing
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Refinement | Resolution: 1.7→10 Å / σ(F): 0 / Stereochemistry target values: X-plor V. 3.8
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Refinement step | Cycle: LAST / Resolution: 1.7→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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