[English] 日本語
Yorodumi- PDB-2qs8: Crystal structure of a Xaa-Pro dipeptidase with bound methionine ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qs8 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a Xaa-Pro dipeptidase with bound methionine in the active site | ||||||
Components | Xaa-Pro Dipeptidase | ||||||
Keywords | HYDROLASE / Amidohydrolase / Dipeptidase / TIM barrel / Protein Structure Initiative / PSI-2 / 9355e / NYSGXRC / Structural Genomics / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | Function and homology information hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / metal ion binding Similarity search - Function | ||||||
Biological species | Alteromonas macleodii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.33 Å | ||||||
Authors | Kumaran, D. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Functional annotation of two new carboxypeptidases from the amidohydrolase superfamily of enzymes. Authors: Xiang, D.F. / Xu, C. / Kumaran, D. / Brown, A.C. / Sauder, J.M. / Burley, S.K. / Swaminathan, S. / Raushel, F.M. | ||||||
History |
| ||||||
Remark 999 | SEQUENCE THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT DATABASE AT THE TIME OF ... SEQUENCE THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT DATABASE AT THE TIME OF DEPOSITION. THE SEQUENCE INFORMATION IS AVAILABLE AT GENBANK WITH ACCESSION CODE GI:88795397. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2qs8.cif.gz | 164.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2qs8.ent.gz | 137.2 KB | Display | PDB format |
PDBx/mmJSON format | 2qs8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qs8_validation.pdf.gz | 448.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2qs8_full_validation.pdf.gz | 459.6 KB | Display | |
Data in XML | 2qs8_validation.xml.gz | 32.7 KB | Display | |
Data in CIF | 2qs8_validation.cif.gz | 46.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qs/2qs8 ftp://data.pdbj.org/pub/pdb/validation_reports/qs/2qs8 | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 46014.914 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alteromonas macleodii (bacteria) / Plasmid: pSGX3(BC) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: K7N5L1*PLUS #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.28 % |
---|---|
Crystal grow | Temperature: 298 K / pH: 7 Details: 30% MPD, 0.1M Hepes pH 7.0, 0.2M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 12, 2007 / Details: MIRRORS |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.33→50 Å / Num. obs: 44488 / % possible obs: 99.8 % / Redundancy: 19 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.33→2.41 Å / Redundancy: 12 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3 / % possible all: 98.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.33→45.81 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 54537.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: RESIDUES LISTED AS MISSING IN REMARK 465 ARE DUE TO LACK OF ELECTRON DENSITY. RESIDUES WITH MISSING ATOMS LISTED IN REMARK 470 ARE DUE TO LACK OF ELECTRON DENSITY FOR SIDE CHAINS AND MODELED AS ALANINES.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 21.08 Å2 / ksol: 0.31 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.7 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.33→45.81 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.33→2.48 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|