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Yorodumi- PDB-7tt9: Crystal structure of Shewanella benthica Group 1 truncated hemogl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tt9 | ||||||
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Title | Crystal structure of Shewanella benthica Group 1 truncated hemoglobin C51S C71S Y34F variant | ||||||
Components | Group 1 truncated hemoglobin | ||||||
Keywords | HEME BINDING PROTEIN / globin / 2/2 hemoglobin / tetramer / piezophilic | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Shewanella benthica KT99 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 2 Å | ||||||
Authors | Martinez, J.E. / Liu, K. / Siegler, M.A. / Schlessman, J.L. / Lecomte, J.T.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal structure of Shewanella benthica Group 1 truncated hemoglobin C51S C71S Y34F variant Authors: Martinez, J.E. / Liu, K. / Siegler, M.A. / Schlessman, J.L. / 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 | 7tt9.cif.gz | 143.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tt9.ent.gz | 90.1 KB | Display | PDB format |
PDBx/mmJSON format | 7tt9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tt9_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 7tt9_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 7tt9_validation.xml.gz | 25.6 KB | Display | |
Data in CIF | 7tt9_validation.cif.gz | 36 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tt/7tt9 ftp://data.pdbj.org/pub/pdb/validation_reports/tt/7tt9 | HTTPS FTP |
-Related structure data
Related structure data | 3aq7S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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-Components
#1: Protein | Mass: 12822.427 Da / Num. of mol.: 4 / Mutation: C51S, C71S, Y34F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella benthica KT99 (bacteria) / Gene: KT99_16901 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A9DF82 #2: Chemical | ChemComp-HEM / #3: 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: 2.06 Å3/Da / Density % sol: 40.4 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M Bis-Tris, pH 6.5, 28% w/v PEG2000 MME |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: Agilent SuperNova / Wavelength: 1.54 Å |
Detector | Type: AGILENT ATLAS CCD / Detector: CCD / Date: Sep 16, 2021 |
Radiation | Monochromator: MIrror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→24.28 Å / Num. obs: 30655 / % possible obs: 99.98 % / Redundancy: 3.04 % / Biso Wilson estimate: 11.95 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.028 / Rrim(I) all: 0.051 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.29 % / Rmerge(I) obs: 0.113 / Mean I/σ(I) obs: 5.8 / Num. unique obs: 5684 / CC1/2: 0.981 / Rpim(I) all: 0.091 / Rrim(I) all: 0.146 / % possible all: 99.84 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: PDB entry 3AQ7 Resolution: 2→23.45 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.41 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 Details: MR-SAD: rough MR solution combined with purely SAD-based structure factors obtained from anomalous data
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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: 14.58 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→23.45 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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