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Yorodumi- PDB-3pvq: Crystal structure of a putative dipeptidyl-peptidase VI (BT_1314)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pvq | ||||||
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Title | Crystal structure of a putative dipeptidyl-peptidase VI (BT_1314) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.10 A resolution | ||||||
Components | Dipeptidyl-peptidase VI | ||||||
Keywords | HYDROLASE / CYSTEINE PROTEINASE FOLD / SH3-LIKE BARREL / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY | ||||||
Function / homology | Function and homology information Bacterial dipeptidyl-peptidase SH3 domain / Bacterial dipeptidyl-peptidase Sh3 domain / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / NlpC/P60 family / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / SH3 Domains / Papain-like cysteine peptidase superfamily / SH3 type barrels. ...Bacterial dipeptidyl-peptidase SH3 domain / Bacterial dipeptidyl-peptidase Sh3 domain / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / NlpC/P60 family / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / SH3 Domains / Papain-like cysteine peptidase superfamily / SH3 type barrels. / Roll / Alpha-Beta Complex / Mainly Beta / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a putative dipeptidyl-peptidase VI (BT_1314) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.10 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pvq.cif.gz | 257.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pvq.ent.gz | 213.1 KB | Display | PDB format |
PDBx/mmJSON format | 3pvq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3pvq_validation.pdf.gz | 448.7 KB | Display | wwPDB validaton report |
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Full document | 3pvq_full_validation.pdf.gz | 453 KB | Display | |
Data in XML | 3pvq_validation.xml.gz | 28.4 KB | Display | |
Data in CIF | 3pvq_validation.cif.gz | 40.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pv/3pvq ftp://data.pdbj.org/pub/pdb/validation_reports/pv/3pvq | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 35653.582 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Strain: VPI-5482 / Gene: BT_1314 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8A860 #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT (RESIDUES 22-328) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 22-328) WAS EXPRESSED WITH A PURIFICATI | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.96 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 20.0% Glycerol, 0.04M KH2PO4, 16.0% PEG-8000, No Buffer pH None, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9537,0.9796 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 15, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.1→29.159 Å / Num. obs: 40250 / % possible obs: 91 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.817 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 6.89 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.1→29.159 Å / Cor.coef. Fo:Fc: 0.9453 / Cor.coef. Fo:Fc free: 0.9298 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 Details: 1. 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 FOR THE REDUCED ...Details: 1. 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. GLYCEROL(GOL) AND CHLORIDE (CL) MODELED ARE PRESENT PROTEIN/CRYSTALLIZATION/CRYO BUFFER. 3. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 4. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 5. THE CYSTEINE RESIDUE (203, 291) ARE OXIDIZED BASED ON THE ELECTRON DENSITY.
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Displacement parameters | Biso max: 108.43 Å2 / Biso mean: 30.5614 Å2 / Biso min: 9.75 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→29.159 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.15 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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