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Yorodumi- PDB-1j8b: Structure of YbaB from Haemophilus influenzae (HI0442), a protein... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j8b | ||||||
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Title | Structure of YbaB from Haemophilus influenzae (HI0442), a protein of unknown function | ||||||
Components | YbaB | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / HI0442 / hypothetical protein / Structure 2 Function Project / S2F | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Haemophilus influenzae Rd (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å | ||||||
Authors | Lim, K. / Tempcyzk, A. / Toedt, J. / Parsons, J.F. / Howard, A. / Eisenstein, E. / Herzberg, O. / Structure 2 Function Project (S2F) | ||||||
Citation | Journal: Proteins / Year: 2003 Title: Crystal structure of YbaB from Haemophilus influenzae (HI0442), a protein of unknown function coexpressed with the recombinational DNA repair protein RecR Authors: Lim, K. / Tempcyzk, A. / Parsons, J.F. / Bonander, N. / Toedt, J. / Kelman, Z. / Howard, A. / Eisenstein, E. / Herzberg, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j8b.cif.gz | 31.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j8b.ent.gz | 24.6 KB | Display | PDB format |
PDBx/mmJSON format | 1j8b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1j8b_validation.pdf.gz | 427.4 KB | Display | wwPDB validaton report |
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Full document | 1j8b_full_validation.pdf.gz | 429 KB | Display | |
Data in XML | 1j8b_validation.xml.gz | 8.1 KB | Display | |
Data in CIF | 1j8b_validation.cif.gz | 11.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j8/1j8b ftp://data.pdbj.org/pub/pdb/validation_reports/j8/1j8b | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | To obtain a dimer, apply -X,Y,1/2-Z symmetry operator and 1,0,1 translation vector |
-Components
#1: Protein | Mass: 12734.129 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae Rd (bacteria) / Species: Haemophilus influenzae / Strain: KW20 / Gene: HI0442 / Plasmid: pET15b-HI0442 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: P44711 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.29 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 3.8 Details: 1 M ammonium phosphate, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9789, 0.9790, 0.9500 | ||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 1, 2000 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.75→99 Å / Num. all: 10936 / Num. obs: 10936 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 18 | ||||||||||||
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.214 / Num. unique all: 810 / % possible all: 73.5 | ||||||||||||
Reflection | *PLUS Lowest resolution: 99 Å / Num. obs: 19416 / Num. measured all: 73832 / Rmerge(I) obs: 0.046 | ||||||||||||
Reflection shell | *PLUS % possible obs: 73.5 % / Rmerge(I) obs: 0.201 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.75→99 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 33 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.83 Å /
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Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 2 / Rfactor Rfree: 0.274 / Rfactor Rwork: 0.185 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.331 / Rfactor Rwork: 0.353 |