[English] 日本語
Yorodumi- PDB-1x42: Crystal structure of a haloacid dehalogenase family protein (PH04... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1x42 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a haloacid dehalogenase family protein (PH0459) from Pyrococcus horikoshii OT3 | ||||||
Components | hypothetical protein PH0459 | ||||||
Keywords | HYDROLASE / haloacid dehalogenase / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information N-acylneuraminate-9-phosphatase activity / N-acetylneuraminate biosynthetic process / dephosphorylation / metal ion binding Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Arai, R. / Kukimoto-Niino, M. / Sugahara, M. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Protein Sci. / Year: 2006 Title: Crystal structure of the probable haloacid dehalogenase PH0459 from Pyrococcus horikoshii OT3 Authors: Arai, R. / Kukimoto-Niino, M. / Kuroishi, C. / Bessho, Y. / Shirouzu, M. / Yokoyama, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1x42.cif.gz | 58.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1x42.ent.gz | 46.4 KB | Display | PDB format |
PDBx/mmJSON format | 1x42.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1x42_validation.pdf.gz | 427.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1x42_full_validation.pdf.gz | 431.5 KB | Display | |
Data in XML | 1x42_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 1x42_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x4/1x42 ftp://data.pdbj.org/pub/pdb/validation_reports/x4/1x42 | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 27092.984 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL-X References: UniProt: O58216, Hydrolases; Acting on halide bonds; In carbon-halide compounds |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.46 % |
---|---|
Crystal grow | Temperature: 293 K / Method: oil batch / pH: 7 Details: 0.1M Tris-HCl, 0.88M tri-Sodium Citrate, pH 7.0, Oil batch, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.97890, 0.97930, 0.96000 | ||||||||||||
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 28, 2004 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
| ||||||||||||
Reflection | Resolution: 2→50 Å / Num. obs: 17044 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3.676 % / Biso Wilson estimate: 6 Å2 / Rsym value: 0.089 / Net I/σ(I): 12.027 | ||||||||||||
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 4.996 / Num. unique all: 1682 / Rsym value: 0.272 / % possible all: 98.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2→42.8 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 976767.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.0682 Å2 / ksol: 0.37847 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.5 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→42.8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|