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- PDB-1e85: Cytochrome c' from Alcaligenes xylosoxidans - reduced structure w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1.0E+85 | |||||||||
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Title | Cytochrome c' from Alcaligenes xylosoxidans - reduced structure with NO bound to proximal side of heme | |||||||||
![]() | CYTOCHROME C' | |||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Lawson, D.M. / Stevenson, C.E.M. / Andrew, C.R. / Eady, R.R. | |||||||||
![]() | ![]() 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: ![]() Title: The Three-Dimensional Structure of Cytochrome C' from Two Alcaligenes Species and Their Implications for Four-Helix Bundles Authors: Dobbs, A.J. / Faber, H.R. / Anderson, B.F. / Baker, E.N. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 45.5 KB | Display | ![]() |
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PDB format | ![]() | 29.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1e83C ![]() 1e84C ![]() 1e86C ![]() 1cgoS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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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) ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-HEC / ![]() | ||
#3: Chemical | ChemComp-NO / ![]() | ||
#4: Water | ChemComp-HOH / ![]() | ||
Compound details | CYTOCHROMESequence details | N-TERMINAL RESIDUE IS PYRROLIDON | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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. ...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 NO. | |||||||||||||||||||||||||
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: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jan 15, 2000 / Details: MIRRORS |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.35→40 Å / Num. obs: 33925 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 39.8 |
Reflection shell | Resolution: 1.35→1.37 Å / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 3.9 / % possible all: 93.1 |
Reflection shell | *PLUS % possible obs: 93.1 % |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1CGO Resolution: 1.35→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.06 Details: FE ATOM OF HEME REFINED WITH ANISOTROPIC THERMAL PARAMETERS
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Displacement parameters | Biso mean: 18 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→40 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.194 / Rfactor Rfree![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |