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Yorodumi- PDB-8vij: Crystal structure of Shewanella benthica Group 1 truncated hemogl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8vij | ||||||
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Title | Crystal structure of Shewanella benthica Group 1 truncated hemoglobin Y34F C51S C71S variant (cyanomet) | ||||||
Components | Group 1 truncated hemoglobin | ||||||
Keywords | HEME-BINDING PROTEIN / GLOBIN / 2/2 HEMOGLOBIN / HEME BINDING PROTEIN / PSYCHROPIEZOPHILE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Shewanella benthica KT99 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 1.35 Å | ||||||
Authors | Lecomte, J.T.J. / Schlessman, J.L. / Martinez, J.E. / Schultz, T.D. / Siegler, M.A. / DelCampo, M. / Le Magueres, P. | ||||||
Funding support | United States, 1items
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Citation | Journal: To be published Title: Crystal structure of Shewanella benthica Group 1 truncated hemoglobin Y34F C51S C71S variant in the cyanomet state Authors: Lecomte, J.T.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8vij.cif.gz | 211.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vij.ent.gz | 170.5 KB | Display | PDB format |
PDBx/mmJSON format | 8vij.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8vij_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 8vij_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8vij_validation.xml.gz | 24.6 KB | Display | |
Data in CIF | 8vij_validation.cif.gz | 35.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vi/8vij ftp://data.pdbj.org/pub/pdb/validation_reports/vi/8vij | 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
#1: Protein | Mass: 12822.427 Da / Num. of mol.: 4 / Mutation: Y34F, C51S, C71S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella benthica KT99 (bacteria) / Strain: KT99 / Gene: KT99_16901 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A9DF82 #2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-CYN / #4: Water | ChemComp-HOH / | 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: 2.09 Å3/Da / Density % sol: 38.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 23% PEG MME 2000, 100 mM Bis-Tris pH 6.5, 10 mM KCN |
-Data collection
Diffraction | Mean temperature: 100 K Ambient temp details: Temperature oscillated and increased to about 105 K first and then 110 K in the last quarter of the experiment. Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54184 Å |
Detector | Type: RIGAKU HyPix-Arc 100 / Detector: PIXEL / Date: Jul 3, 2022 |
Radiation | Monochromator: Rigaku VariMax DW optics (confocal multilayer) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54184 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→18.97 Å / Num. obs: 97066 / % possible obs: 99 % / Redundancy: 5 % / Biso Wilson estimate: 7.83 Å2 / Rsym value: 0.081 / Net I/σ(I): 11.02 |
Reflection shell | Resolution: 1.35→1.4 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 3.46 / Num. unique obs: 9662 / Rsym value: 0.286 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.35→16.97 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 0.8 / Phase error: 18.45 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→16.97 Å
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Refine LS restraints |
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LS refinement shell |
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