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Yorodumi- PDB-1izm: Structure of ygfB from Haemophilus influenzae (HI0817), a Conserv... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1izm | ||||||
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Title | Structure of ygfB from Haemophilus influenzae (HI0817), a Conserved Hypothetical Protein | ||||||
Components | HYPOTHETICAL PROTEIN HI0817Hypothesis | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / hypothetical protein / HI0817 / ygfB / Structure 2 Function Project / S2F | ||||||
Function / homology | YgfB uncharacterised protein family PF03695 / YgfB-like / YgfB-like superfamily / Uncharacterised protein family (UPF0149) / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / cytosol / UPF0149 protein HI_0817 Function and homology information | ||||||
Biological species | Haemophilus influenzae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å | ||||||
Authors | Galkin, A. / Sarikaya, E. / Lehmann, C. / Howard, A. / Herzberg, O. / Structure 2 Function Project (S2F) | ||||||
Citation | Journal: Proteins / Year: 2004 Title: X-ray structure of HI0817 from Haemophilus influenzae: protein of unknown function with a novel fold. Authors: Galkin, A. / Sarikaya, E. / Lehmann, C. / 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 | 1izm.cif.gz | 51.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1izm.ent.gz | 36.5 KB | Display | PDB format |
PDBx/mmJSON format | 1izm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iz/1izm ftp://data.pdbj.org/pub/pdb/validation_reports/iz/1izm | 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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1 |
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Unit cell |
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Details | Dimer.The asymmetric unit contains one monomer. The dimer is generated from the monomer by a crystallographic symmetry: Y-1, X+1,-Z+1 |
-Components
#1: Protein | Mass: 20604.152 Da / Num. of mol.: 1 / Mutation: L8M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: HI0817 / Plasmid: pET100 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P44882 |
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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: 2.15 Å3/Da / Density % sol: 42.92 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 1.4 M ammonimum sulfate, 0.05 M potassium phosphate, 3% iso-propanol, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
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: 0.97946, 0.97961, 0.96863 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 6, 2001 | ||||||||||||
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: 1.95→20 Å / Num. all: 14167 / Num. obs: 14167 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.05 / Net I/σ(I): 21.1 | ||||||||||||
Reflection shell | Resolution: 1.95→2.02 Å / Rmerge(I) obs: 0.097 / % possible all: 91.9 | ||||||||||||
Reflection | *PLUS Num. obs: 24638 / % possible obs: 98 % / Num. measured all: 298675 / Rmerge(I) obs: 0.05 | ||||||||||||
Reflection shell | *PLUS % possible obs: 92 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.95→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 38 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.02 Å
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Refine LS restraints | *PLUS Type: c_bond_d / Dev ideal: 0.02 |