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Open data
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Basic information
Entry | Database: PDB / ID: 1vhb | ||||||
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Title | BACTERIAL DIMERIC HEMOGLOBIN FROM VITREOSCILLA STERCORARIA | ||||||
![]() | HEMOGLOBIN | ||||||
![]() | OXYGEN TRANSPORT / HEME / RESPIRATORY PROTEIN | ||||||
Function / homology | ![]() nitric oxide dioxygenase NAD(P)H activity / cellular response to nitrosative stress / nitric oxide catabolic process / FAD binding / oxygen carrier activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Tarricone, C. / Galizzi, A. / Coda, A. / Ascenzi, P. / Bolognesi, M. | ||||||
![]() | ![]() Title: Unusual structure of the oxygen-binding site in the dimeric bacterial hemoglobin from Vitreoscilla sp. Authors: Tarricone, C. / Galizzi, A. / Coda, A. / Ascenzi, P. / Bolognesi, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 67.9 KB | Display | ![]() |
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PDB format | ![]() | 50.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 14.3 KB | Display | |
Data in CIF | ![]() | 19.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given / Matrix: (0.26808, -0.9634), |
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Components
#1: Protein | Mass: 15790.269 Da / Num. of mol.: 2 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: 2.3 Å3/Da / Density % sol: 48 % | ||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / pH: 6.4 Details: PRECIPITANT: AMMONIUM SULFATE 1.2 M. BUFFER: PYROPHOSPHATE 0.2 M PH 6.4. ADDITIVES: ETHYLENE GLYCOL 3% V/V. PROTEIN CONCENTRATION 25 MG/ML. VAPOR DIFFUSION TECHNIQUES., vapor diffusion | ||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→25 Å / Num. obs: 26582 / % possible obs: 94.9 % / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.36 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.83→1.88 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2 / Rsym value: 0.36 / % possible all: 61 |
Reflection | *PLUS Num. measured all: 101071 |
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Processing
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Refinement | Method to determine structure: SIR-DENSITY MODIFICATION / Resolution: 1.83→15 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: A POSTERIORI / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
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Solvent computation | Bsol: 167 Å2 / ksol: 0.58 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.83→15 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.184 / Rfactor Rfree: 0.254 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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