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Yorodumi- PDB-1jog: Structure of HI0074 from Heamophilus Influenzae reveals the fold ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jog | ||||||
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Title | Structure of HI0074 from Heamophilus Influenzae reveals the fold of a substrate binding domain of a nucleotidyltransferase | ||||||
Components | HYPOTHETICAL PROTEIN HI0074 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / HI0074 / hypothetical protein / Structure 2 Function Project / S2F | ||||||
Function / homology | Probable ribonuclease HepT / Nucleotidyltransferase substrate binding protein like / Nucleotidyltransferases domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / Uncharacterized protein HI_0074 Function and homology information | ||||||
Biological species | Haemophilus influenzae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å | ||||||
Authors | Lehmann, C. / Lim, K. / Herzberg, O. / Structure 2 Function Project (S2F) | ||||||
Citation | Journal: Proteins / Year: 2003 Title: The HI0073/HI0074 protein pair from Haemophilus influenzae is a member of a new nucleotidyltransferase family: Structure, sequence analyses, and solution studies Authors: Lehmann, C. / Lim, K. / Chalamasetty, V.R. / Krajewski, W. / Melamud, E. / Galkin, A. / Howard, A. / Kelman, Z. / Reddy, P.T. / Murzin, A.G. / Herzberg, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jog.cif.gz | 118.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jog.ent.gz | 100.8 KB | Display | PDB format |
PDBx/mmJSON format | 1jog.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jog_validation.pdf.gz | 461.5 KB | Display | wwPDB validaton report |
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Full document | 1jog_full_validation.pdf.gz | 493.8 KB | Display | |
Data in XML | 1jog_validation.xml.gz | 26.5 KB | Display | |
Data in CIF | 1jog_validation.cif.gz | 36.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jo/1jog ftp://data.pdbj.org/pub/pdb/validation_reports/jo/1jog | 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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2 |
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Unit cell |
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Details | Probably a dimer. The asymmetric unit contains two dimers. |
-Components
#1: Protein | Mass: 17518.633 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: HI0074 / Plasmid: pRE1 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P43934 #2: 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: 1.97 Å3/Da / Density % sol: 37.59 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 30% PEG 4000, 0.1 M Tris, 0.2 M Na acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 0.9791, 0.9793, 1.00 | ||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 30, 2001 / Details: mirror | ||||||||||||
Radiation | Monochromator: Si (111) double crystal system / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.4→30 Å / Num. all: 22467 / Num. obs: 22467 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 6.8 | ||||||||||||
Reflection shell | Resolution: 2.4→2.51 Å / Rmerge(I) obs: 0.314 / % possible all: 100 | ||||||||||||
Reflection | *PLUS Lowest resolution: 30 Å |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.4→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 57 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.49 Å / Rfactor Rfree: 0.334 / Rfactor Rwork: 0.258 | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 2.1 |