+Open data
-Basic information
Entry | Database: PDB / ID: 7vle | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Oxy-deoxy intermediate of V2 hemoglobin at 55% oxygen saturation | |||||||||
Components | (Extracellular ...) x 4 | |||||||||
Keywords | OXYGEN TRANSPORT / allostery / structural transition / giant hemoglobin | |||||||||
Function / homology | Function and homology information hemoglobin complex / oxygen carrier activity / oxygen binding / response to hypoxia / iron ion binding / heme binding / extracellular region Similarity search - Function | |||||||||
Biological species | Lamellibrachia satsuma (invertebrata) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Numoto, N. / Onoda, S. / Kawano, Y. / Okumura, H. / Baba, S. / Fukumori, Y. / Miki, K. / Ito, N. | |||||||||
Funding support | Japan, 2items
| |||||||||
Citation | Journal: Biophys Physicobio. / Year: 2022 Title: Structures of oxygen dissociation intermediates of 400 kDa V2 hemoglobin provide coarse snapshots of the protein allostery. Authors: Numoto, N. / Onoda, S. / Kawano, Y. / Okumura, H. / Baba, S. / Fukumori, Y. / Miki, K. / Ito, N. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7vle.cif.gz | 255.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7vle.ent.gz | 202.8 KB | Display | PDB format |
PDBx/mmJSON format | 7vle.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vle_validation.pdf.gz | 4.9 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7vle_full_validation.pdf.gz | 4.9 MB | Display | |
Data in XML | 7vle_validation.xml.gz | 48.7 KB | Display | |
Data in CIF | 7vle_validation.cif.gz | 63.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vl/7vle ftp://data.pdbj.org/pub/pdb/validation_reports/vl/7vle | HTTPS FTP |
-Related structure data
Related structure data | 7vlcC 7vldC 7vlfC 3wctS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
-Extracellular ... , 4 types, 8 molecules AEBFCGDH
#1: Protein | Mass: 16368.704 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Lamellibrachia satsuma (invertebrata) / References: UniProt: S0BBU7 #2: Protein | Mass: 15951.922 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Lamellibrachia satsuma (invertebrata) / References: UniProt: S0BBR6 #3: Protein | Mass: 16519.531 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Lamellibrachia satsuma (invertebrata) / References: UniProt: S0BCU7 #4: Protein | Mass: 16228.627 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Lamellibrachia satsuma (invertebrata) / References: UniProt: S0BAP9 |
---|
-Sugars , 1 types, 2 molecules
#5: Polysaccharide | Source method: isolated from a genetically manipulated source |
---|
-Non-polymers , 3 types, 332 molecules
#6: Chemical | ChemComp-HEM / #7: Chemical | ChemComp-OXY / #8: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.81 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 14-17% (w/v) PEG 3350, 100mM HEPES-NaOH pH 7.5 |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 1, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 58863 / % possible obs: 99.9 % / Redundancy: 11.1 % / Biso Wilson estimate: 43.79 Å2 / CC1/2: 0.999 / Rsym value: 0.122 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.3→2.44 Å / Redundancy: 9.1 % / Mean I/σ(I) obs: 1.8 / CC1/2: 0.584 / Rsym value: 1.32 / % possible all: 99.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WCT Resolution: 2.3→48.87 Å / SU ML: 0.3388 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.6298 / Stereochemistry target values: GeoStd + Monomer Library
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.83 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→48.87 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|