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Yorodumi- PDB-4o23: Crystal structure of mono-zinc form of succinyl diaminopimelate d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4o23 | ||||||
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Title | Crystal structure of mono-zinc form of succinyl diaminopimelate desuccinylase from Neisseria meningitidis MC58 | ||||||
Components | Succinyl-diaminopimelate desuccinylase | ||||||
Keywords | HYDROLASE / DapE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Function and homology information acetylornithine deacetylase activity / succinyl-diaminopimelate desuccinylase / succinyl-diaminopimelate desuccinylase activity / arginine biosynthetic process / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / cobalt ion binding / zinc ion binding Similarity search - Function | ||||||
Biological species | Neisseria meningitidis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å | ||||||
Authors | Nocek, B. / Holz, R. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: Biochemistry / Year: 2015 Title: Inhibition of the dapE-Encoded N-Succinyl-L,L-diaminopimelic Acid Desuccinylase from Neisseria meningitidis by L-Captopril. Authors: Starus, A. / Nocek, B. / Bennett, B. / Larrabee, J.A. / Shaw, D.L. / Sae-Lee, W. / Russo, M.T. / Gillner, D.M. / Makowska-Grzyska, M. / 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 | 4o23.cif.gz | 304.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4o23.ent.gz | 247.5 KB | Display | PDB format |
PDBx/mmJSON format | 4o23.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4o23_validation.pdf.gz | 441.8 KB | Display | wwPDB validaton report |
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Full document | 4o23_full_validation.pdf.gz | 445.1 KB | Display | |
Data in XML | 4o23_validation.xml.gz | 30.6 KB | Display | |
Data in CIF | 4o23_validation.cif.gz | 44 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o2/4o23 ftp://data.pdbj.org/pub/pdb/validation_reports/o2/4o23 | HTTPS FTP |
-Related structure data
Related structure data | 4ppzC 4pqaC 1vgyS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 41645.875 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: MC58 / Gene: dapE, NMB1530 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9JYL2, succinyl-diaminopimelate desuccinylase #2: Chemical | #3: Chemical | #4: 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: 2.45 Å3/Da / Density % sol: 49.83 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M Succinic Acid, 15% PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-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: Nov 27, 2013 / 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: 2.09→39.25 Å / Num. all: 49315 / Num. obs: 48738 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 18 |
Reflection shell | Resolution: 2.09→2.14 Å / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1VGY Resolution: 2.09→39.25 Å / SU ML: 0.22 / σ(F): 1.35 / σ(I): 1.5 / Phase error: 25.74 / Stereochemistry target values: ML
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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: 2.09→39.25 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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