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- PDB-3g53: Ligand migration and cavities within scapharca dimeric hemoglobin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3g53 | ||||||
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Title | Ligand migration and cavities within scapharca dimeric hemoglobin: wild type with co bound to heme and chloropropyl benzene bound to the XE4 cavity | ||||||
![]() | Globin-1 | ||||||
![]() | OXYGEN BINDING / OXYGEN TRANSPORT / ALLOSTERY / OXYGEN AFFINITY / CYTOPLASM / HEME / IRON / METAL-BINDING / OXYGEN STORAGE/TRANSPORT | ||||||
Function / homology | ![]() oxygen carrier activity / oxygen binding / response to hypoxia / heme binding / identical protein binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Knapp, J.E. / Pahl, R. / Cohen, J. / Nichols, J.C. / Schulten, K. / Gibson, Q.H. / Srajer, V. / Royer Jr., W.E. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.3 KB | Display | ![]() |
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PDB format | ![]() | 55.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3g46C ![]() 3g4qC ![]() 3g4rC ![]() 3g4uC ![]() 3g4vC ![]() 3g4wC ![]() 3g4yC ![]() 3g52C ![]() 3sdhS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15967.304 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-LT1 / ( | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.5 % |
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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: 295 K |
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Diffraction source | Source: ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.5501 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.64→39.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.64→1.74 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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