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Yorodumi- PDB-6qpu: Crystal structure of as isolated synthetic core domain of nitrite... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qpu | |||||||||
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Title | Crystal structure of as isolated synthetic core domain of nitrite reductase from Ralstonia pickettii (residues 1-331) | |||||||||
Components | Copper-containing nitrite reductase | |||||||||
Keywords | METAL BINDING PROTEIN / synthetic core domain / nitrite reductase / inter-copper electron transfer | |||||||||
Function / homology | Function and homology information nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / periplasmic space / electron transfer activity / copper ion binding / heme binding Similarity search - Function | |||||||||
Biological species | Ralstonia sp. 5_2_56FAA (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | |||||||||
Authors | Antonyuk, S.V. / Hedison, T.M. / Eady, R.R. / Hasnain, S.S. / Scrutton, N.S. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Acs Catalysis / Year: 2019 Title: Unexpected Roles of a Tether Harboring a Tyrosine Gatekeeper Residue in Modular Nitrite Reductase Catalysis. Authors: Hedison, T.M. / Shenoy, R.T. / Iorgu, A.I. / Heyes, D.J. / Fisher, K. / Wright, G.S.A. / Hay, S. / Eady, R.R. / Antonyuk, S.V. / Hasnain, S.S. / Scrutton, N.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qpu.cif.gz | 734.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qpu.ent.gz | 609.8 KB | Display | PDB format |
PDBx/mmJSON format | 6qpu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qpu_validation.pdf.gz | 483.6 KB | Display | wwPDB validaton report |
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Full document | 6qpu_full_validation.pdf.gz | 495.6 KB | Display | |
Data in XML | 6qpu_validation.xml.gz | 76.6 KB | Display | |
Data in CIF | 6qpu_validation.cif.gz | 110.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qp/6qpu ftp://data.pdbj.org/pub/pdb/validation_reports/qp/6qpu | HTTPS FTP |
-Related structure data
Related structure data | 6qptC 6qpvC 6qpxC 6qpzC 6qq0C 6qq1C 6qq2C 3ziyS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 35611.352 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ralstonia sp. 5_2_56FAA (bacteria) / Gene: HMPREF0989_00586 / Cell line (production host): BL21 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: U3G913, nitrite reductase (NO-forming) #2: Chemical | ChemComp-CU / #3: Chemical | ChemComp-CL / #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 2.35 Å3/Da / Density % sol: 47.6 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6 Details: containing 0.2 MgCl2, 20% P6000 in MES buffer pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å |
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Sep 7, 2018 |
Radiation | Monochromator: FRE+ / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→45.6 Å / Num. obs: 84912 / % possible obs: 94.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 25.5 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.076 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.25→2.3 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 1.4 / CC1/2: 0.541 / Rpim(I) all: 0.53 / % possible all: 75.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ziy Resolution: 2.25→42.68 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.925 / SU B: 14.596 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.354 / ESU R Free: 0.238 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.131 Å2
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Refinement step | Cycle: 1 / Resolution: 2.25→42.68 Å
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Refine LS restraints |
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