[English] 日本語
Yorodumi- PDB-1e86: Cytochrome c' from Alcaligenes xylosoxidans - reduced structure w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1.0E+86 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cytochrome c' from Alcaligenes xylosoxidans - reduced structure with CO bound to distal side of heme | |||||||||
Components | CYTOCHROME C' | |||||||||
Keywords | ELECTRON TRANSPORT / CYTOCHROME / HEME / 4-HELIX BUNDLE / CARBON MONOXIDE | |||||||||
Function / homology | Function and homology information electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding Similarity search - Function | |||||||||
Biological species | ALCALIGENES XYLOSOXIDANS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1e86.cif.gz | 44.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1e86.ent.gz | 28.9 KB | Display | PDB format |
PDBx/mmJSON format | 1e86.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1e86_validation.pdf.gz | 794.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1e86_full_validation.pdf.gz | 796.8 KB | Display | |
Data in XML | 1e86_validation.xml.gz | 9.8 KB | Display | |
Data in CIF | 1e86_validation.cif.gz | 13.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e8/1e86 ftp://data.pdbj.org/pub/pdb/validation_reports/e8/1e86 | HTTPS FTP |
-Related structure data
Related structure data | 1e83C 1e84C 1e85C 1cgoS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-HEC / | ||||||
#3: Chemical | #4: Water | ChemComp-HOH / | Compound details | CYTOCHROME | Sequence details | N-TERMINAL RESIDUE IS PYRROLIDON | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.3 % | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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. ...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. REDUCED USING MOTHER LIQUOR CONTAINING 20 MM SODIUM DITHIONITE, THEN INCUBATED FOR 6 DAYS IN MOTHER LIQUOR SATURATED WITH CO. | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.2 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1999 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→40 Å / Num. obs: 12158 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 9.9 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 33.2 |
Reflection shell | Resolution: 1.95→2.02 Å / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 5.8 / % possible all: 86.8 |
Reflection shell | *PLUS % possible obs: 86.8 % / Rmerge(I) obs: 0.31 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CGO Resolution: 1.95→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.16 Details: FE ATOM OF HEME REFINED WITH ANISOTROPIC THERMAL PARAMETERS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→40 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.203 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |