[English] 日本語
Yorodumi- PDB-3qob: Mechanical Coupling Controls Cooperative Ligand Binding in a Homo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qob | ||||||
---|---|---|---|---|---|---|---|
Title | Mechanical Coupling Controls Cooperative Ligand Binding in a Homodimeric Hemoglobin | ||||||
Components | Globin-1 | ||||||
Keywords | OXYGEN TRANSPORT / time-resolved / Laue diffraction / dynamic crystallography / heterogeneous structure | ||||||
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 | Anadara inaequivalvis (ark clam) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å | ||||||
Authors | Ren, Z. | ||||||
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 Jr., W.E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3qob.cif.gz | 62.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3qob.ent.gz | 45 KB | Display | PDB format |
PDBx/mmJSON format | 3qob.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qob_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3qob_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3qob_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 3qob_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qo/3qob ftp://data.pdbj.org/pub/pdb/validation_reports/qo/3qob | HTTPS FTP |
-Related structure data
Related structure data | 3ugyC 3ugzC 3uh3C 3uh5C 3uh6C 3uh7C 3uhbC 3uhcC 3uhdC 3uheC 3uhgC 3uhhC 3uhiC 3uhkC 3uhnC 3uhqC 3uhrC 3uhsC 3uhtC 3uhuC 3uhvC 3uhwC 3uhxC 3uhyC 3uhzC 3ui0C 3sdhS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 15966.319 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Anadara inaequivalvis (ark clam) / References: UniProt: P02213 #2: Chemical | #3: Chemical | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.88 % |
---|
-Data collection
Diffraction | Mean temperature: 288 K | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.017 - 1.2 | |||||||||
Detector | Type: MAR CCD 165 mm / Detector: AREA DETECTOR / Date: Nov 6, 2008 | |||||||||
Radiation | Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray | |||||||||
Radiation wavelength |
| |||||||||
Reflection | Resolution: 1.6→38.2 Å / Num. all: 27862 / Num. obs: 27844 / % possible obs: 74.5 % / Observed criterion σ(F): 6 / Redundancy: 3.27 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.0597 / Net I/σ(I): 24.7 |
-Processing
Software |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 3SDH Resolution: 1.6→38.2 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 6 / Stereochemistry target values: Engh & Huber /
| ||||||||||||
Displacement parameters | Biso max: 20 Å2 / Biso mean: 20 Å2 / Biso min: 20 Å2 | ||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→38.2 Å
|