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Yorodumi- PDB-1no5: Structure of HI0073 from Haemophilus influenzae, the nucleotide b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1no5 | ||||||
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Title | Structure of HI0073 from Haemophilus influenzae, the nucleotide binding domain of the HI0073/HI0074 two protein nucleotidyl transferase. | ||||||
Components | Hypothetical protein HI0073Hypothesis | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / HI0073 / HI0074 / nucleotidyl transferase / Structure 2 Function Project / S2F | ||||||
Function / homology | Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / nucleotidyltransferase activity / Nucleotidyltransferase superfamily / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein HI_0073 Function and homology information | ||||||
Biological species | Haemophilus influenzae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Lehmann, C. / Pullalarevu, S. / Galkin, A. / Krajewski, W. / Willis, M.A. / Howard, A. / Herzberg, O. / Structure 2 Function Project (S2F) | ||||||
Citation | Journal: Proteins / Year: 2005 Title: Structure of HI0073 from Haemophilus influenzae, the nucleotide-binding domain of a two-protein nucleotidyl transferase Authors: Lehmann, C. / Pullalarevu, S. / Krajewski, W. / Willis, M.A. / Galkin, A. / Howard, A. / Herzberg, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1no5.cif.gz | 65.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1no5.ent.gz | 46.7 KB | Display | PDB format |
PDBx/mmJSON format | 1no5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/no/1no5 ftp://data.pdbj.org/pub/pdb/validation_reports/no/1no5 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 13196.114 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: HI0073 / Plasmid: pHI0073 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: P43933 |
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-Non-polymers , 5 types, 316 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-GOL / | #4: Chemical | #5: Chemical | ChemComp-NA / | #6: 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: 2.2 Å3/Da / Density % sol: 54.39 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10% 2-Propanol, 0.1 M Sodium cacodylate, 0.2 M Zn(acetate)2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 173 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 0.98 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 13, 2002 / Details: mirror |
Radiation | Monochromator: Si(111) double crystal system / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→19.79 Å / Num. all: 51005 / Num. obs: 51005 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.028 / Net I/σ(I): 32.14 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 5 / Num. unique all: 2558 / % possible all: 100 |
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 19.8 Å / % possible obs: 0.028 % / Num. measured all: 960910 |
Reflection shell | *PLUS Lowest resolution: 1.85 Å / % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→19.79 Å / Num. parameters: 7935 / Num. restraintsaints: 6841 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 1 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1975 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→19.79 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 19.8 Å / Rfactor obs: 0.201 / Rfactor Rwork: 0.2 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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