+Open data
-Basic information
Entry | Database: PDB / ID: 3uht | ||||||
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Title | HBI (L36V) deoxy | ||||||
Components | Globin-1 | ||||||
Keywords | OXYGEN STORAGE / OXYGEN TRANSPORT / allostery / oxygen binding | ||||||
Function / homology | Function and homology information oxygen carrier activity / oxygen binding / response to hypoxia / heme binding / identical protein binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Scapharca inaequivalvis (ark clam) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Ren, Z. / Srajer, V. / Knapp, J.E. / Royer Jr., W.E. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Cooperative macromolecular device revealed by meta-analysis of static and time-resolved structures. Authors: Ren, Z. / Srajer, V. / Knapp, J.E. / Royer, W.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3uht.cif.gz | 74.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uht.ent.gz | 55.5 KB | Display | PDB format |
PDBx/mmJSON format | 3uht.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3uht_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3uht_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3uht_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 3uht_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uh/3uht ftp://data.pdbj.org/pub/pdb/validation_reports/uh/3uht | HTTPS FTP |
-Related structure data
Related structure data | 3qobC 3ugyC 3ugzC 3uh3C 3uh5C 3uh6C 3uh7C 3uhbC 3uhcC 3uhdC 3uheC 3uhgC 3uhhC 3uhiC 3uhkC 3uhnC 3uhqC 3uhrC 3uhsC 3uhuC 3uhvC 3uhwC 3uhxC 3uhyC 3uhzC 3ui0C 4sdhS 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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Unit cell |
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-Components
#1: Protein | Mass: 15953.276 Da / Num. of mol.: 2 / Mutation: L36V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Scapharca inaequivalvis (ark clam) / Plasmid: PCS-26 / Production host: Escherichia coli (E. coli) / Strain (production host): W3110LACIQ L8 / References: UniProt: P02213 #2: Chemical | #3: 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: 2.3 Å3/Da / Density % sol: 46.46 % |
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Crystal grow | Temperature: 298 K / Method: small tubes / pH: 8.5 Details: 1.5-2.5 M phosphate, pH 8.50, SMALL TUBES, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 10, 2005 |
Radiation | Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. all: 20330 / Num. obs: 19029 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 12.3 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 4.1 / Rsym value: 0.267 / % possible all: 82.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4SDH Resolution: 2→26.75 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2263713 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.8645 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→26.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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