[English] 日本語
Yorodumi- PDB-3ocw: Structure of Recombinant Haemophilus influenzae e(P4) Acid Phosph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ocw | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of Recombinant Haemophilus influenzae e(P4) Acid Phosphatase mutant D66N complexed with 3'-AMP | ||||||
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: 1.85 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3ocw.cif.gz | 70.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3ocw.ent.gz | 49.5 KB | Display | PDB format |
PDBx/mmJSON format | 3ocw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oc/3ocw ftp://data.pdbj.org/pub/pdb/validation_reports/oc/3ocw | HTTPS FTP |
---|
-Related structure data
Related structure data | 3ocuC 3ocvC 3ocxC 3ocyC 3et4S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 29619.998 Da / Num. of mol.: 1 / Mutation: D66N 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 |
---|---|
#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-3AM / [( |
#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 |
---|
-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.2 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 23-28% (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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: NOIR-1 / Detector: CCD / Date: Jan 21, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: beamline optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.85→50 Å / Num. obs: 26166 / % possible obs: 99.9 % / Redundancy: 20.5 % / Rmerge(I) obs: 0.114 / Χ2: 0.779 / Net I/σ(I): 7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3et4 Resolution: 1.85→44.884 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.889 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.964 Å2 / ksol: 0.366 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 60.08 Å2 / Biso mean: 17.6541 Å2 / Biso min: 5.22 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→44.884 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9
|