+Open data
-Basic information
Entry | Database: PDB / ID: 1.0E+83 | |||||||||
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Title | Cytochrome c' from Alcaligenes xylosoxidans - oxidized structure | |||||||||
Components | CYTOCHROME C' | |||||||||
Keywords | ELECTRON TRANSPORT / HEME / 4-HELIX BUNDLE | |||||||||
Function / homology | Function and homology information electron transfer activity / periplasmic space / iron ion binding / heme binding Similarity search - Function | |||||||||
Biological species | ALCALIGENES XYLOSOXIDANS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | |||||||||
Authors | Lawson, D.M. / Stevenson, C.E.M. / Andrew, C.R. / Eady, R.R. | |||||||||
Citation | Journal: Embo J. / Year: 2000 Title: Unprecedented Proximal Binding of Nitric Oxide to Heme: Implications for Guanylate Cyclase Authors: Lawson, D.M. / Stevenson, C.E.M. / Andrew, C.R. / Eady, R.R. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1996 Title: Three-Dimensional Structure of Cytochrome C' from Two Alcaligenes Species and the Implications for Four-Helix Bundle Structures. Authors: Dobbs, A.J. / Anderson, B.F. / Faber, H.R. / Baker, E.N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e83.cif.gz | 44.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e83.ent.gz | 29.2 KB | Display | PDB format |
PDBx/mmJSON format | 1e83.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e8/1e83 ftp://data.pdbj.org/pub/pdb/validation_reports/e8/1e83 | HTTPS FTP |
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-Related structure data
Related structure data | 1e84C 1e85C 1e86C 1cgoS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13631.442 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: FORMERLY KNOWN AS ALCALIGENES SP. / Source: (natural) ALCALIGENES XYLOSOXIDANS (bacteria) / Cellular location: PERIPLASM / Strain: NCIB 11015 / References: UniProt: P00138 | ||
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#2: Chemical | ChemComp-HEC / | ||
#3: Water | ChemComp-HOH / | ||
Compound details | CYTOCHROMESequence details | N-TERMINAL RESIDUE IS PYRROLIDON | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.3 % | |||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: HANGING DROP VAPOUR DIFFUSION. PROTEIN AT CONCENTRATION 8 MG/ML WAS MIXED WITH AN EQUAL VOLUME OF WELL SOLUTION CONSISTING OF 55-65% SATURATED AMMONIUM SULFATE IN 100 MM HEPES BUFFER AT PH 7.5 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.2 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
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: SRS / Beamline: PX7.2 / Wavelength: 1.488 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1997 / Details: MIRRORS |
Radiation | Monochromator: GE(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→40 Å / Num. obs: 10205 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 2.05→2.12 Å / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 5.2 / % possible all: 98.9 |
Reflection shell | *PLUS % possible obs: 98.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CGO Resolution: 2.05→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.18 Details: FE ATOM OF HEME REFINED WITH ANISOTROPIC THERMAL PARAMETERS
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Displacement parameters | Biso mean: 23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→40 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.192 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |