+Open data
-Basic information
Entry | Database: PDB / ID: 1i77 | ||||||
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Title | CYTOCHROME C3 FROM DESULFOVIBRIO DESULFURICANS ESSEX 6 | ||||||
Components | CYTOCHROME C3 | ||||||
Keywords | ELECTRON TRANSPORT / multi-heme cytochrome c | ||||||
Function / homology | Function and homology information electron transfer activity / periplasmic space / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Desulfovibrio desulfuricans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Einsle, O. / Foerster, S. / Mann, K.H. / Fritz, G. / Messerschmidt, A. / Kroneck, P.M.H. | ||||||
Citation | Journal: Eur.J.Biochem. / Year: 2001 Title: Spectroscopic investigation and determination of reactivity and structure of the tetraheme cytochrome c3 from Desulfovibrio desulfuricans Essex 6. Authors: Einsle, O. / Foerster, S. / Mann, K. / Fritz, G. / Messerschmidt, A. / Kroneck, P.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i77.cif.gz | 41 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i77.ent.gz | 28.3 KB | Display | PDB format |
PDBx/mmJSON format | 1i77.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i7/1i77 ftp://data.pdbj.org/pub/pdb/validation_reports/i7/1i77 | HTTPS FTP |
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-Related structure data
Related structure data | 2cyr 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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Unit cell |
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-Components
#1: Protein | Mass: 11637.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Desulfovibrio desulfuricans (bacteria) / Strain: ESSEX 6 / References: UniProt: Q9L915 | ||
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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: 2.74 Å3/Da / Density % sol: 55.08 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: PEG MME 2000, sodium acetate, ammonium sulfate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 3, 1997 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→18 Å / Num. all: 9821 / Num. obs: 9654 / % possible obs: 98.3 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.8 % / Biso Wilson estimate: 25.98 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 1.95→2.01 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 3.1 / % possible all: 98.5 |
Reflection | *PLUS Num. measured all: 59364 |
Reflection shell | *PLUS % possible obs: 98.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CYR 2cyr Resolution: 1.95→18 Å / Isotropic thermal model: Isotropic / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 29.92 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→18 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 18 Å / σ(F): 2 / Rfactor obs: 0.173 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |