+Open data
-Basic information
Entry | Database: PDB / ID: 8gar | ||||||
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Title | Nitrosomonas europaea Cytochrome P460 Arg44Ala | ||||||
Components | Cytochrome P460 | ||||||
Keywords | METAL BINDING PROTEIN / Cytochrome / Heme protein | ||||||
Function / homology | Cytochrome P460 / Cytochrome P460 superfamily / Cytochrome P460 / metal ion binding / ACETATE ION / HEME C / Cytochrome P460 Function and homology information | ||||||
Biological species | Nitrosomonas europaea (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Bollmeyer, M.M. / Lancaster, K.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2023 Title: Cytochrome P460 Cofactor Maturation Proceeds via Peroxide-Dependent Post-translational Modification. Authors: Bollmeyer, M.M. / Coleman, R.E. / Majer, S.H. / Ferrao, S.D. / Lancaster, K.M. #1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gar.cif.gz | 123.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gar.ent.gz | 82.7 KB | Display | PDB format |
PDBx/mmJSON format | 8gar.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gar_validation.pdf.gz | 863 KB | Display | wwPDB validaton report |
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Full document | 8gar_full_validation.pdf.gz | 863 KB | Display | |
Data in XML | 8gar_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 8gar_validation.cif.gz | 13.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ga/8gar ftp://data.pdbj.org/pub/pdb/validation_reports/ga/8gar | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-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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-Components
#1: Protein | Mass: 21236.994 Da / Num. of mol.: 1 / Mutation: R44A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nitrosomonas europaea (bacteria) / Gene: cyp / Production host: Escherichia coli (E. coli) / References: UniProt: Q50927 |
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#2: Chemical | ChemComp-HEC / |
#3: Chemical | ChemComp-ACT / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG 3000, calcium acetate, sodium cacodylate, MOP buffer |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 1, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→46.0157 Å / Num. obs: 30693 / % possible obs: 99.68 % / Redundancy: 19.8 % / Biso Wilson estimate: 25.3002206217 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.05202 / Rrim(I) all: 0.05344 / Net I/σ(I): 32.17 |
Reflection shell | Resolution: 1.55→1.605 Å / Redundancy: 20.2 % / Rmerge(I) obs: 1.518 / Mean I/σ(I) obs: 2.11 / Num. unique obs: 3014 / CC1/2: 0.916 / CC star: 0.978 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→46.0157 Å / SU ML: 0.185834184717 / Cross valid method: FREE R-VALUE / σ(F): 1.34973758215 / Phase error: 22.6285976111 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.5325967268 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→46.0157 Å
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Refine LS restraints |
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LS refinement shell |
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