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Yorodumi- PDB-5xev: Crystal Structure of a novel Xaa-Pro dipeptidase from Deinococcus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xev | ||||||
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Title | Crystal Structure of a novel Xaa-Pro dipeptidase from Deinococcus radiodurans | ||||||
Components | Xaa-Pro dipeptidase,Peptidase-related protein | ||||||
Keywords | HYDROLASE / Xaa-Pro dipeptidase / prolidase / M28B peptidase / Deinococcus radiodurans | ||||||
Function / homology | Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / aminopeptidase activity / peptidase activity / cytosol / ACETATE ION / PHOSPHATE ION / Peptidase-related protein Function and homology information | ||||||
Biological species | Deinococcus radiodurans R1 (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Are, V.N. / Kumar, A. / Ghosh, B. / Makde, R.D. | ||||||
Citation | Journal: Proteins / Year: 2017 Title: Crystal structure of a novel prolidase from Deinococcus radiodurans identifies new subfamily of bacterial prolidases. Authors: Are, V.N. / Jamdar, S.N. / Ghosh, B. / Goyal, V.D. / Kumar, A. / Neema, S. / Gadre, R. / Makde, R.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xev.cif.gz | 251.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xev.ent.gz | 204.8 KB | Display | PDB format |
PDBx/mmJSON format | 5xev.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xe/5xev ftp://data.pdbj.org/pub/pdb/validation_reports/xe/5xev | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 45308.289 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus radiodurans R1 (radioresistant) Plasmid: pST50STRHIS Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422 Gene: DR_0478 / Details (production host): T7 based expression plasmid / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9RX37, Xaa-Pro dipeptidase |
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-Non-polymers , 6 types, 423 molecules
#2: Chemical | #3: Chemical | ChemComp-PO4 / | #4: Chemical | ChemComp-ACT / | #5: Chemical | ChemComp-CL / | #6: Chemical | ChemComp-EDO / | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | This protein corresponds to database(UniParc:UPI0002D66B97,GenBank:ANC72273). |
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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: 2.45 Å3/Da / Density % sol: 49.72 % |
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Crystal grow | Temperature: 294 K / Method: microbatch / pH: 4.8 Details: 40 mM KH2PO4, 10mM ammonium citrate, pH 4.8, 3 mM phenylalanine, 1 mM MnCl2, 10 mM ZnCl2, 16% PEG8000, 20% Glycerol PH range: 4.5-5.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97947 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 29, 2016 / Details: Mirrors |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97947 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→45.94 Å / Num. obs: 85429 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.027 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.789 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4196 / CC1/2: 0.757 / Rpim(I) all: 0.331 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→31.955 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.77
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→31.955 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -21.9916 Å / Origin y: -21.9256 Å / Origin z: 1.6981 Å
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Refinement TLS group | Selection details: all |