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Yorodumi- PDB-4op4: Crystal structure of the catalytic domain of DapE protein from V.... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4op4 | |||||||||
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Title | Crystal structure of the catalytic domain of DapE protein from V.cholerea in the Zn bound form | |||||||||
Components | Succinyl-diaminopimelate desuccinylase | |||||||||
Keywords | HYDROLASE / aminopeptidase / M20 / CSGID / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases | |||||||||
Function / homology | Function and homology information succinyl-diaminopimelate desuccinylase / succinyl-diaminopimelate desuccinylase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / cobalt ion binding / zinc ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Vibrio cholerae O1 biovar El Tor (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.651 Å | |||||||||
Authors | Nocek, B. / Makowska-Grzyska, M. / Jedrzejczak, R. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | |||||||||
Citation | Journal: Plos One / Year: 2014 Title: The Dimerization Domain in DapE Enzymes Is required for Catalysis. Authors: Nocek, B. / Starus, A. / Makowska-Grzyska, M. / Gutierrez, B. / Sanchez, S. / Jedrzejczak, R. / Mack, J.C. / Olsen, K.W. / Joachimiak, A. / Holz, R.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4op4.cif.gz | 212.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4op4.ent.gz | 168.6 KB | Display | PDB format |
PDBx/mmJSON format | 4op4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4op4_validation.pdf.gz | 466.8 KB | Display | wwPDB validaton report |
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Full document | 4op4_full_validation.pdf.gz | 470.8 KB | Display | |
Data in XML | 4op4_validation.xml.gz | 26.1 KB | Display | |
Data in CIF | 4op4_validation.cif.gz | 39.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/op/4op4 ftp://data.pdbj.org/pub/pdb/validation_reports/op/4op4 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 28676.559 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria) Strain: N16961 / Gene: dapE, VC_2152 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9KQ52, succinyl-diaminopimelate desuccinylase |
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-Non-polymers , 5 types, 531 molecules
#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-ZN / #4: Chemical | #5: Chemical | ChemComp-BU1 / #6: 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: 2.9 Å3/Da / Density % sol: 57.65 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 20% (V/V) 1,4-BUTANEDIOL 0.1 M ACETATE, PH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 14, 2011 / Details: mirrors |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→40 Å / Num. all: 70716 / Num. obs: 70716 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.051 |
Reflection shell | Resolution: 1.65→1.68 Å / % possible all: 49.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.651→37.714 Å / σ(F): 0 / σ(I): 0 / Phase error: 16.74 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.651→37.714 Å
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Refine LS restraints |
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LS refinement shell |
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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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