+Open data
-Basic information
Entry | Database: PDB / ID: 3uhu | ||||||
---|---|---|---|---|---|---|---|
Title | HBI (M37A) 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: 2.1 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3uhu.cif.gz | 68.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3uhu.ent.gz | 50.9 KB | Display | PDB format |
PDBx/mmJSON format | 3uhu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uh/3uhu ftp://data.pdbj.org/pub/pdb/validation_reports/uh/3uhu | 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 3uhtC 3uhvC 3uhwC 3uhxC 3uhyC 3uhzC 3ui0C 4sdhS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 15907.185 Da / Num. of mol.: 2 / Mutation: M37A 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 / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.7 % |
---|---|
Crystal grow | Temperature: 298 K / Method: small tubes / pH: 7.5 / Details: phosphate, pH 7.5, SMALL TUBES, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 24, 2003 |
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: 2.1→50 Å / Num. all: 17668 / Num. obs: 16414 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 12.7 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.1→2.18 Å / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 3.8 / Rsym value: 0.232 / % possible all: 93.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4SDH Resolution: 2.1→30.74 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2214389.93 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.9279 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.5 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→30.74 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|