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- PDB-4onw: Crystal structure of the catalytic domain of DapE protein from V.... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4onw | |||||||||
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Title | Crystal structure of the catalytic domain of DapE protein from V.cholerea | |||||||||
![]() | Succinyl-diaminopimelate desuccinylase | |||||||||
![]() | HYDROLASE / DapE / M20 / aminopeptidase / CSGID / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / Zn binding | |||||||||
Function / homology | ![]() 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 | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Nocek, B. / Makowska-Grzyska, M. / Jedrzejczak, R. / Gu, M. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 129.1 KB | Display | ![]() |
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PDB format | ![]() | 99 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 476.9 KB | Display | ![]() |
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Full document | ![]() | 481.9 KB | Display | |
Data in XML | ![]() | 27.5 KB | Display | |
Data in CIF | ![]() | 41.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4h2kC ![]() 4op4C ![]() 3iszS S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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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.) ![]() Strain: N16961 / Gene: dapE, VC_2152 / Plasmid: pMCSG7 / Production host: ![]() ![]() References: UniProt: Q9KQ52, succinyl-diaminopimelate desuccinylase |
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-Non-polymers , 5 types, 554 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/BU1.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BU1.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-BU1 / #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-ACT / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.37 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 20% (V/V) 1,4-BUTANEDIOL, 0.1M Acetate,, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
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 twin |
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Reflection | Resolution: 1.65→37.6 Å / Num. all: 77006 / Num. obs: 77006 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 30 | |||||||||||||||
Reflection shell | Resolution: 1.65→1.68 Å / % possible all: 93.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3ISZ Resolution: 1.65→37.6 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.902 / SU ML: 0.033 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.015 / ESU R Free: 0.016 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.514 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→37.6 Å
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Refine LS restraints |
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