[English] 日本語
Yorodumi- PDB-3g53: Ligand migration and cavities within scapharca dimeric hemoglobin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3g53 | ||||||
---|---|---|---|---|---|---|---|
Title | Ligand migration and cavities within scapharca dimeric hemoglobin: wild type with co bound to heme and chloropropyl benzene bound to the XE4 cavity | ||||||
Components | Globin-1 | ||||||
Keywords | OXYGEN BINDING / OXYGEN TRANSPORT / ALLOSTERY / OXYGEN AFFINITY / CYTOPLASM / HEME / IRON / METAL-BINDING / OXYGEN STORAGE/TRANSPORT | ||||||
Function / homology | Function and homology information oxygen carrier activity / oxygen binding / heme binding / identical protein binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Anadara inaequivalvis (ark clam) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.64 Å | ||||||
Authors | Knapp, J.E. / Pahl, R. / Cohen, J. / Nichols, J.C. / Schulten, K. / Gibson, Q.H. / Srajer, V. / Royer Jr., W.E. | ||||||
Citation | Journal: Structure / Year: 2009 Title: Ligand migration and cavities within Scapharca Dimeric HbI: studies by time-resolved crystallo-graphy, Xe binding, and computational analysis. Authors: Knapp, J.E. / Pahl, R. / Cohen, J. / Nichols, J.C. / Schulten, K. / Gibson, Q.H. / Srajer, V. / Royer, W.E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3g53.cif.gz | 75.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3g53.ent.gz | 55.3 KB | Display | PDB format |
PDBx/mmJSON format | 3g53.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g5/3g53 ftp://data.pdbj.org/pub/pdb/validation_reports/g5/3g53 | HTTPS FTP |
---|
-Related structure data
Related structure data | 3g46C 3g4qC 3g4rC 3g4uC 3g4vC 3g4wC 3g4yC 3g52C 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: 15967.304 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anadara inaequivalvis (ark clam) / Plasmid: PCS-26 / Production host: Escherichia coli (E. coli) / Strain (production host): W3110LACIQL8 / References: UniProt: P02213 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-LT1 / ( | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.5 % |
---|---|
Crystal grow | Temperature: 296 K / Method: microbatch / pH: 7.5 Details: 1.5-2.5M PHOSPHATE BUFFER, PH 7.50, SMALL TUBES, TEMPERATURE 298K, Microbatch, temperature 296K |
-Data collection
Diffraction | Mean temperature: 295 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 / Wavelength: 1.54 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 19, 2004 / Details: OSMIC MIRRORS |
Radiation | Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→100 Å / Num. all: 34934 / Num. obs: 34586 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 1.64→1.76 Å / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 4.2 / Rsym value: 0.333 / % possible all: 98.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3SDH Resolution: 1.64→39.57 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1216405.08 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Details: BULK SOLVENT MODEL USED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.5501 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.9 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.64→39.57 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.64→1.74 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|