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Yorodumi- PDB-8qvb: Crystal structure of chlorite dismutase at 3000 eV based on a com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qvb | ||||||
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Title | Crystal structure of chlorite dismutase at 3000 eV based on a combination of spherical harmonics and analytical absorption corrections | ||||||
Components | Chlorite Dismutase | ||||||
Keywords | OXIDOREDUCTASE / long-wavelength x-ray diffraction | ||||||
Function / homology | Heme-dependent peroxidase ChdC/CLD / Chlorite dismutase / Dimeric alpha-beta barrel / oxidoreductase activity / heme binding / metal ion binding / PROTOPORPHYRIN IX CONTAINING FE / Chlorite dismutase Function and homology information | ||||||
Biological species | Cyanothece sp. PCC 7425 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Duman, R. / Wagner, A. / Kamps, J. / Orville, A. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J.Appl.Crystallogr. / Year: 2024 Title: Ray-tracing analytical absorption correction for X-ray crystallography based on tomographic reconstructions. Authors: Lu, Y. / Duman, R. / Beilsten-Edmands, J. / Winter, G. / Basham, M. / Evans, G. / Kamps, J.J.A.G. / Orville, A.M. / Kwong, H.S. / Beis, K. / Armour, W. / Wagner, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qvb.cif.gz | 92.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qvb.ent.gz | 69.3 KB | Display | PDB format |
PDBx/mmJSON format | 8qvb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qvb_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 8qvb_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 8qvb_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 8qvb_validation.cif.gz | 21.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qv/8qvb ftp://data.pdbj.org/pub/pdb/validation_reports/qv/8qvb | HTTPS FTP |
-Related structure data
Related structure data | 8quqC 8qurC 8quuC 8quvC 8quzC 8qvsC 8qvvC C: citing same article (ref.) |
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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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 21830.881 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cyanothece sp. PCC 7425 (bacteria) / Gene: Cyan7425_1434 / Production host: Escherichia coli (E. coli) / References: UniProt: B8HNS6 |
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-Non-polymers , 5 types, 60 molecules
#2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
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: 2.91 Å3/Da / Density % sol: 57.79 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 150mM MgSO4, 100mM MES, pH 6.5 and 20 % w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 4.132 Å |
Detector | Type: DECTRIS PILATUS 12M / Detector: PIXEL / Date: May 16, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 4.132 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50.35 Å / Num. obs: 13696 / % possible obs: 99.43 % / Redundancy: 41.1 % / CC1/2: 0.999 / Net I/σ(I): 44.73 |
Reflection shell | Resolution: 2.7→2.797 Å / Num. unique obs: 1351 / CC1/2: 0.993 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→50.35 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.916 / SU B: 8.916 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 1.473 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 29.439 Å2
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Refinement step | Cycle: 1 / Resolution: 2.7→50.35 Å
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