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Yorodumi- PDB-5zum: Structure of dipeptidyl-peptidase III from Corallococcus sp. stra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zum | ||||||
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Title | Structure of dipeptidyl-peptidase III from Corallococcus sp. strain EGB | ||||||
Components | dipeptidyl-peptidase III | ||||||
Keywords | HYDROLASE / metallopeptidase | ||||||
Function / homology | Peptidase family M49 / Peptidase family M49 / hydrolase activity / metal ion binding / Dipeptidyl-peptidase III Function and homology information | ||||||
Biological species | Corallococcus sp. EGB (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å | ||||||
Authors | Zhang, H. / Duan, Y.J. / Li, Z.K. / Liu, W.D. / Huang, Y. / Cui, Z.L. | ||||||
Citation | Journal: To Be Published Title: Structure of dipeptidyl peptidase III from Corallococcus sp. strain EGB Authors: Zhang, H. / Duan, Y.J. / Li, Z.K. / Liu, W.D. / Huang, Y. / Cui, Z.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zum.cif.gz | 233.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zum.ent.gz | 193 KB | Display | PDB format |
PDBx/mmJSON format | 5zum.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zum_validation.pdf.gz | 433.8 KB | Display | wwPDB validaton report |
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Full document | 5zum_full_validation.pdf.gz | 440.7 KB | Display | |
Data in XML | 5zum_validation.xml.gz | 46.7 KB | Display | |
Data in CIF | 5zum_validation.cif.gz | 70.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zu/5zum ftp://data.pdbj.org/pub/pdb/validation_reports/zu/5zum | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 59584.391 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corallococcus sp. EGB (bacteria) / Strain: EGB / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5H1ZR28*PLUS #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.17 Å3/Da / Density % sol: 43.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.59 Details: 24%(w/v) PEG 3350, 0.1M sodium cacodylate acetate trihydrate pH 4.59, 0.02M TCEP hydrochioride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 8, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→25 Å / Num. obs: 82472 / % possible obs: 99.7 % / Redundancy: 5.3 % / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.9→9.87 Å |
-Processing
Software |
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Refinement | Resolution: 1.9→25 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.359 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.149 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.216 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→25 Å
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Refine LS restraints |
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