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Yorodumi- PDB-7zs8: Mixed-valence, active form, of cytochrome c peroxidase from oblig... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zs8 | |||||||||
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Title | Mixed-valence, active form, of cytochrome c peroxidase from obligate human pathogenic bacterium Neisseria gonorrhoeae at 1.4 Angstrom resolution | |||||||||
Components | Cytochrome-c peroxidase | |||||||||
Keywords | ELECTRON TRANSPORT / Neisseria gonorrhoeae / bacterial peroxidase / ROS detoxification | |||||||||
Function / homology | Function and homology information cytochrome-c peroxidase / cytochrome-c peroxidase activity / periplasmic space / electron transfer activity / heme binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Neisseria gonorrhoeae (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | |||||||||
Authors | Carvalho, A.L. / Romao, M.J. / Pauleta, S. / Nobrega, C. | |||||||||
Funding support | Portugal, 2items
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Citation | Journal: Int J Mol Sci / Year: 2023 Title: Structural Characterization of Neisseria gonorrhoeae Bacterial Peroxidase-Insights into the Catalytic Cycle of Bacterial Peroxidases. Authors: Nobrega, C.S. / Carvalho, A.L. / Romao, M.J. / Pauleta, S.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zs8.cif.gz | 157.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zs8.ent.gz | 122 KB | Display | PDB format |
PDBx/mmJSON format | 7zs8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zs8_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 7zs8_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 7zs8_validation.xml.gz | 31.3 KB | Display | |
Data in CIF | 7zs8_validation.cif.gz | 46.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zs/7zs8 ftp://data.pdbj.org/pub/pdb/validation_reports/zs/7zs8 | HTTPS FTP |
-Related structure data
Related structure data | 6fu3S 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
#1: Protein | Mass: 36302.875 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: ccpA, E8M64_00570, ERS135259_00627, NCTC13484_01765 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1D3HIT0, cytochrome-c peroxidase #2: Chemical | ChemComp-HEC / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.1 Å3/Da / Density % sol: 43.84 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion Details: 0.1 M MES pH 6.0, 30 % 5/4 PO/OH, 2 mM CaCl2, 10 mM sodium ascorbate and 0.2 mM FMN |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 29, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→39.95 Å / Num. obs: 124619 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.4→1.42 Å / Rmerge(I) obs: 0.0656 / Num. unique obs: 6083 / CC1/2: 0.813 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6fu3 Resolution: 1.4→39.95 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.368 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.07 / 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: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.815 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→39.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
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