[English] 日本語
Yorodumi- PDB-2hsz: Crystal structure of a predicted phosphoglycolate phosphatase (hs... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hsz | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a predicted phosphoglycolate phosphatase (hs_0176) from haemophilus somnus 129pt at 1.90 A resolution | ||||||
Components | novel predicted phosphatase | ||||||
Keywords | HYDROLASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Function and homology information phosphoglycolate phosphatase / phosphoglycolate phosphatase activity / glycolate biosynthetic process / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Haemophilus somnus 129PT (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of novel predicted phosphatase from Haemophilus somnus 129PT at 1.90 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
| ||||||
Remark 300 | REMARK 300 BIOMOLECULE: 1,2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS ...REMARK 300 BIOMOLECULE: 1,2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY DATA SUPPORTS THE ASSIGNMENT OF A MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE. | ||||||
Remark 999 | SEQUENCE A suitable database reference was not available at the time of processing. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2hsz.cif.gz | 107.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2hsz.ent.gz | 86.2 KB | Display | PDB format |
PDBx/mmJSON format | 2hsz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2hsz_validation.pdf.gz | 441.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2hsz_full_validation.pdf.gz | 443.1 KB | Display | |
Data in XML | 2hsz_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 2hsz_validation.cif.gz | 31.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hs/2hsz ftp://data.pdbj.org/pub/pdb/validation_reports/hs/2hsz | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
2 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: MSE / End label comp-ID: GLN / Refine code: 4 / Auth seq-ID: 1 - 224 / Label seq-ID: 20 - 243
| ||||||||||||||||||
Details | SIZE EXCLUSION CHROMATOGRAPHY DATA SUPPORTS THE ASSIGNMENT OF A MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE |
-Components
#1: Protein | Mass: 27552.707 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus somnus 129PT (bacteria) / Species: Histophilus somni / Production host: Escherichia coli (E. coli) / References: UniProt: Q0I1W8 #2: Chemical | #3: Chemical | #4: Chemical | Num. of mol.: 2 / Source method: obtained synthetically #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 57.68 % |
---|---|
Crystal grow | Temperature: 277 K / pH: 7.9 Details: 0.2M NaAcetate, 20.0% PEG-3350, No Buffer pH 7.9, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97925,1.28281,0.97914 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 8, 2006 / Details: Flat collimating mirror, toroid focusing mirror | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.897→29.988 Å / Num. obs: 51412 / % possible obs: 100 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 6.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: MAD |
---|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 1.9→29.988 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.066 / SU ML: 0.076 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.112 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: (1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN ...Details: (1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. (3). THERE ARE UNKNOWN DENSITY NEAR ACTIVE SITE IN A AND B CHAINS. THEY ARE NAMED AS UNL. (4). THERE ARE UNKNOWN DENSITY NEAR PHE 75 IN A AND B MOLECULES, TYR 77 AND PHE 138 IN A MOLECULE, PRO 152 AND TYR 200 IN B MOLECULE. THEY ARE ALL IN THE SOLVENT REGION AND LEFT UNMODELED. (5). ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY.
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.69 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→29.988 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2896 / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.901→1.95 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 0 - 224 / Label seq-ID: 19 - 243
|