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Yorodumi- PDB-1m6z: Crystal structure of reduced recombinant cytochrome c4 from Pseud... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m6z | ||||||
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Title | Crystal structure of reduced recombinant cytochrome c4 from Pseudomonas stutzeri | ||||||
Components | Cytochrome c4 | ||||||
Keywords | ELECTRON TRANSPORT / diheme protein | ||||||
Function / homology | Function and homology information electron transfer activity / periplasmic space / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Pseudomonas stutzeri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Noergaard, A. / Harris, P. / Larsen, S. / Christensen, H.E.M. | ||||||
Citation | Journal: To be Published Title: Structural comparison of recombinant Pseudomonas stutzeri cytochrome c4 in two oxidation states Authors: Noergaard, A. / Harris, P. / Larsen, S. / Christensen, H.E.M. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1995 Title: Crystallization and preliminary crystallographic investigations of cytochrome c4 from Pseudomonas stutzeri Authors: Kadziola, A. / Larsen, S. / Christensen, H.M. / Karlsson, J.-J. / Ulstrup, J. #2: Journal: Structure / Year: 1997 Title: Crystal structure of the dihaem cytochrome c4 from Pseudomonas stutzeri determined at 2.2 A resolution Authors: Kadziola, A. / Larsen, S. #3: Journal: HANDBOOK OF METALLOPROTEINS / Year: 2001 Title: Cytochrome c4 Authors: Andersen, N.H. / Christensen, H.E.M. / Iversen, G. / Noergaard, A. / Scharnagl, C. / Thuesen, M.H. / Ulstrup, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m6z.cif.gz | 335.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m6z.ent.gz | 274.8 KB | Display | PDB format |
PDBx/mmJSON format | 1m6z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m6/1m6z ftp://data.pdbj.org/pub/pdb/validation_reports/m6/1m6z | HTTPS FTP |
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-Related structure data
Related structure data | 1m70C 1etpS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 19700.062 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Plasmid: pNM185 / Production host: Pseudomonas putida (bacteria) / Strain (production host): PaW340 / References: UniProt: Q52369 #2: Chemical | ChemComp-HEC / #3: Chemical | #4: Chemical | ChemComp-TRS / | #5: 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: 1.75 Å3/Da / Density % sol: 29.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.6 Details: 0.2M ammonium acetate, 0.1M sodium citrate pH 5.6, 30%(w/v) PEG 4000, 5%(v/v) glycerol, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.0326 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 26, 2001 / Details: Mirror |
Radiation | Monochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0326 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→30 Å / Num. all: 144067 / Num. obs: 142653 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.35→1.4 Å / % possible all: 87 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1ETP Resolution: 1.35→30 Å / Num. parameters: 59868 / Num. restraintsaints: 87330 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Anisotropic refinement. Riding H-atoms introduced.
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 24 / Occupancy sum hydrogen: 5369.27 / Occupancy sum non hydrogen: 6570.54 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→30 Å
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Refine LS restraints |
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