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- PDB-2z85: Ligand Migration and Binding in The Dimeric Hemoglobin of Scaphar... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2z85 | ||||||
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Title | Ligand Migration and Binding in The Dimeric Hemoglobin of Scapharca Inaequivalvis: M37F Unliganded | ||||||
![]() | Globin-1 | ||||||
![]() | OXYGEN BINDING / ALLOSTERY / OXYGEN AFFINITY / COOPERATIVE HEMOGLOBIN / Cytoplasm / Heme / Iron / Metal-binding / Oxygen transport / Transport / 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. / Royer Jr., W.E. / Nienhaus, K. / Palladino, P. / Nienhaus, G.U. | ||||||
![]() | ![]() Title: Ligand Migration and Binding in the Dimeric Hemoglobin of Scapharca inaequivalvis Authors: Nienhaus, K. / Knapp, J.E. / Palladino, P. / Royer Jr., W.E. / Nienhaus, G.U. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 77.7 KB | Display | ![]() |
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PDB format | ![]() | 58 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 15.7 KB | Display | |
Data in CIF | ![]() | 21.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2r4wC ![]() 2r4xC ![]() 2r4yC ![]() 2r4zC ![]() 2z8aC ![]() 4sdhS 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: 15983.282 Da / Num. of mol.: 2 / Mutation: M37F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44 % |
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Crystal grow | Temperature: 298 K / Method: small tubes / pH: 8.5 Details: 1.5-2.5M PHOSPHATE, pH 8.50, SMALL TUBES, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 21, 2003 / Details: OSMIC MIRRORS |
Radiation | Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→40 Å / Num. obs: 36509 / % possible obs: 92.4 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 24.3 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 22.1 |
Reflection shell | Resolution: 1.6→1.66 Å / Rmerge(I) obs: 0.225 / Mean I/σ(I) obs: 4.9 / Rsym value: 0.225 / % possible all: 87.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4SDH Resolution: 1.6→38.69 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1475944.69 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.0975 Å2 / ksol: 0.365804 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 20.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→38.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.59→1.65 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 10
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Xplor file |
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