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Yorodumi- PDB-7zs4: F32V Cytochrome c prime beta from Methylococcus capsulatus (Bath) -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zs4 | ||||||
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Title | F32V Cytochrome c prime beta from Methylococcus capsulatus (Bath) | ||||||
Components | Cytochrome c | ||||||
Keywords | OXIDOREDUCTASE / Cytochrome c prime / Beta-sheet | ||||||
Function / homology | Cytochrome P460 / Cytochrome P460 superfamily / Cytochrome P460 / metal ion binding / HEME C / DI(HYDROXYETHYL)ETHER / Cytochrome c Function and homology information | ||||||
Biological species | Methylococcus capsulatus str. Bath (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Adams, H.R. / Hough, M.A. | ||||||
Funding support | 1items
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Citation | Journal: J.Biol.Chem. / Year: 2023 Title: A heme pocket aromatic quadrupole modulates gas binding to cytochrome c'-beta : Implications for NO sensors. Authors: Adams, H.R. / Svistunenko, D.A. / Wilson, M.T. / Fujii, S. / Strange, R.W. / Hardy, Z.A. / Vazquez, P.A. / Dabritz, T. / Streblow, G.J. / Andrew, C.R. / Hough, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zs4.cif.gz | 75.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zs4.ent.gz | 54.5 KB | Display | PDB format |
PDBx/mmJSON format | 7zs4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zs4_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7zs4_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7zs4_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 7zs4_validation.cif.gz | 19.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zs/7zs4 ftp://data.pdbj.org/pub/pdb/validation_reports/zs/7zs4 | HTTPS FTP |
-Related structure data
Related structure data | 7zpsC 7zqzC 7zrwC 7zrxC 7zsvC 7zswC 7zsxC 7ztiC 7zvzC 6hihS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 3 - 138 / Label seq-ID: 23 - 158
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 17322.607 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methylococcus capsulatus str. Bath (bacteria) Strain: ATCC 33009 / NCIMB 11132 / Bath / Gene: ccp, MCA2394 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G1UBD5 |
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-Non-polymers , 5 types, 144 molecules
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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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: 2.8 Å3/Da / Density % sol: 56.4 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 2 microlitres of 15 mg/ml protein in 0.1 M HEPES buffer, pH 7.5, mixed with with an equivalent volume of reservoir solution containing 0.01 M ZnSO4, 30% PEG 550 (v/v) and 0.1 M MES, pH 6.5. ...Details: 2 microlitres of 15 mg/ml protein in 0.1 M HEPES buffer, pH 7.5, mixed with with an equivalent volume of reservoir solution containing 0.01 M ZnSO4, 30% PEG 550 (v/v) and 0.1 M MES, pH 6.5. Cryoprotection in ML plus 10% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å | ||||||||||||||||||
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 1, 2020 | ||||||||||||||||||
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 1.75→74.72 Å / Num. obs: 40057 / % possible obs: 100 % / Redundancy: 6.6 % / Rpim(I) all: 0.028 / Rrim(I) all: 0.073 / Net I/σ(I): 17.4 | ||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 6.8 % / % possible all: 100
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6HIH Resolution: 1.75→74.71 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.104 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100.01 Å2 / Biso mean: 33.055 Å2 / Biso min: 22.67 Å2
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Refinement step | Cycle: final / Resolution: 1.75→74.71 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 4169 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.75→1.786 Å / Rfactor Rfree error: 0
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