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Yorodumi- PDB-3ocy: Structure of Recombinant Haemophilus Influenzae e(P4) Acid Phosph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ocy | ||||||
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Title | Structure of Recombinant Haemophilus Influenzae e(P4) Acid Phosphatase Complexed with inorganic phosphate | ||||||
Components | Lipoprotein E | ||||||
Keywords | HYDROLASE / outer membrane | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Haemophilus influenzae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Singh, H. / Schuermann, J. / Reilly, T. / Calcutt, M. / Tanner, J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Recognition of nucleoside monophosphate substrates by Haemophilus influenzae class C acid phosphatase. Authors: Singh, H. / Schuermann, J.P. / Reilly, T.J. / Calcutt, M.J. / Tanner, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ocy.cif.gz | 121.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ocy.ent.gz | 92.7 KB | Display | PDB format |
PDBx/mmJSON format | 3ocy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oc/3ocy ftp://data.pdbj.org/pub/pdb/validation_reports/oc/3ocy | HTTPS FTP |
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-Related structure data
Related structure data | 3ocuC 3ocvC 3ocwC 3ocxC 3et4S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 29620.982 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: periplasmic / Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: hel, HI_0693, ompP4 / Plasmid: pET20b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: P26093, acid phosphatase |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
Sequence details | G30E SEQUENCE CONFLICT IN UNP ENTRY P26093 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 18-23 % (w/v) PEG 3350, 0.05-0.2 M ammonium citrate dibasic, 0.05-0.15 mM MgCl2, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 26, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.4→50 Å / Num. obs: 57486 / % possible obs: 95.9 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.064 / Χ2: 1.059 / Net I/σ(I): 8.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3et4 Resolution: 1.4→30.701 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.9251 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.418 Å2 / ksol: 0.429 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 53.22 Å2 / Biso mean: 15.4758 Å2 / Biso min: 5.34 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→30.701 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21
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