+Open data
-Basic information
Entry | Database: PDB / ID: 3gjb | ||||||
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Title | CytC3 with Fe(II) and alpha-ketoglutarate | ||||||
Components | CytC3 | ||||||
Keywords | BIOSYNTHETIC PROTEIN / CytC3 / halogenase / beta barrel | ||||||
Function / homology | Function and homology information Chlorinating enzyme / q2cbj1_9rhob like domain / Phytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / Jelly Rolls / Sandwich / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | Streptomyces sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å | ||||||
Authors | Wong, C. / Drennan, C.L. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2009 Title: Structural analysis of an open active site conformation of nonheme iron halogenase CytC3 Authors: Wong, C. / Fujimori, D.G. / Walsh, C.T. / Drennan, C.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gjb.cif.gz | 125.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gjb.ent.gz | 97 KB | Display | PDB format |
PDBx/mmJSON format | 3gjb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gj/3gjb ftp://data.pdbj.org/pub/pdb/validation_reports/gj/3gjb | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 36484.574 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. (bacteria) / Strain: pSPHE02 / Gene: cytC3 / Plasmid: pET28b / Production host: escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D0VX22*PLUS |
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-Non-polymers , 5 types, 232 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-ACT / #5: Chemical | #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: 3.37 Å3/Da / Density % sol: 63.5 % |
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Crystal grow | Temperature: 298 K / pH: 7 Details: 2.8 M sodium acetate trihydrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 1, 2006 / Details: INTER-IMAGE DEAD TIME 5S |
Radiation | Monochromator: SIDE SCATTERING BENT CUBE- ROOT I-BEAM SINGLE CRYSTAL Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 50583 / % possible obs: 97.6 % / Redundancy: 11 % / Rmerge(I) obs: 0.082 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.48 / % possible all: 81.3 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→44.49 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
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Solvent computation | Bsol: 62.81 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.04 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→44.49 Å
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Refine LS restraints |
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Xplor file |
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