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Yorodumi- PDB-3g46: Ligand migration and cavities within scapharca dimeric hemoglobin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3g46 | ||||||
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Title | Ligand migration and cavities within scapharca dimeric hemoglobin: wild type with co bound to heme and chloroform bound to the XE4 cavity | ||||||
Components | Globin-1 | ||||||
Keywords | OXYGEN BINDING / OXYGEN TRANSPORT / ALLOSTERY / OXYGEN AFFINITY / CYTOPLASM / HEME / IRON / METAL-BINDING / OXYGEN STORAGE/TRANSPORT / 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 | Scapharca inaequivalvis (ark clam) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.91 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3g46.cif.gz | 155 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g46.ent.gz | 121.2 KB | Display | PDB format |
PDBx/mmJSON format | 3g46.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g4/3g46 ftp://data.pdbj.org/pub/pdb/validation_reports/g4/3g46 | HTTPS FTP |
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-Related structure data
Related structure data | 3g4qC 3g4rC 3g4uC 3g4vC 3g4wC 3g4yC 3g52C 3g53C 3sdhS 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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Details | BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. APPLY THE FOLLOWING TO CHAINS: A, B BIOMT1 1 1.000000 0.000000 0.000000 0.00000 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 |
-Components
#1: Protein | Mass: 15967.304 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Scapharca inaequivalvis (ark clam) / Gene: HBI / Plasmid: PCS-26 / Production host: Escherichia coli (E. coli) / Strain (production host): W3110LACIQL8 / References: UniProt: P02213 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-XE / #5: 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: 2.12 Å3/Da / Density % sol: 42 % |
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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: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 7, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 0.91→46.3 Å / Num. all: 205646 / Num. obs: 160199 / % possible obs: 77.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 20 |
Reflection shell | Resolution: 0.91→1.01 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.189 / Mean I/σ(I) obs: 4.7 / Rsym value: 0.189 / % possible all: 59.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3SDH Resolution: 0.91→46.3 Å / Num. parameters: 26633 / Num. restraintsaints: 33906 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Refine analyze | Luzzati coordinate error obs: 0.155 Å / Num. disordered residues: 34 / Occupancy sum hydrogen: 2315.44 / Occupancy sum non hydrogen: 2761.87 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.91→46.3 Å
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Refine LS restraints |
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