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Yorodumi- PDB-2vhb: AZIDE ADDUCT OF THE BACTERIAL HEMOGLOBIN FROM VITREOSCILLA STERCORARIA -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vhb | ||||||
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Title | AZIDE ADDUCT OF THE BACTERIAL HEMOGLOBIN FROM VITREOSCILLA STERCORARIA | ||||||
Components | HEMOGLOBIN | ||||||
Keywords | OXYGEN TRANSPORT / HEME / RESPIRATORY PROTEIN | ||||||
Function / homology | Function and homology information oxygen carrier activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Vitreoscilla stercoraria (bacteria) | ||||||
Method | X-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 1.76 Å | ||||||
Authors | Tarricone, C. / Galizzi, A. / Coda, A. / Ascenzi, P. / Bolognesi, M. | ||||||
Citation | Journal: Structure / Year: 1997 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vhb.cif.gz | 70.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vhb.ent.gz | 52.5 KB | Display | PDB format |
PDBx/mmJSON format | 2vhb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vh/2vhb ftp://data.pdbj.org/pub/pdb/validation_reports/vh/2vhb | HTTPS FTP |
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-Related structure data
-Links
-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: (0.24016, -0.00448, -0.97072), Vector: |
-Components
#1: Protein | Mass: 15790.269 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vitreoscilla stercoraria (bacteria) / Strain: C1 / Gene: VGB / Plasmid: PDH88 / Gene (production host): VGB / Production host: Escherichia coli (E. coli) / Strain (production host): DH5-ALPHA / References: UniProt: P04252 #2: Chemical | #3: Chemical | #4: 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: 2.3 Å3/Da / Density % sol: 52 % | ||||||||||||||||||||
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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. AZIDE SOAKING ...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. AZIDE SOAKING CONDITIONS: 0.03 M N3-, 1 HOUR, PH 7.0, vapor diffusion | ||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Wavelength: 1 |
Detector | Type: MAR RESEARCH 180MM IMAGE PLATE / Detector: IMAGE PLATE AREA DETECTOR / Date: Oct 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→15 Å / Num. obs: 29076 / % possible obs: 94 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 22 |
Reflection shell | Resolution: 1.76→1.83 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 2 / Rsym value: 0.049 / % possible all: 94.1 |
Reflection | *PLUS Num. measured all: 68840 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER / Resolution: 1.76→15 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.76→15 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.197 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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