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Yorodumi- PDB-5m47: Crystal structure of DapF from Corynebacterium glutamicum in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5m47 | |||||||||
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Title | Crystal structure of DapF from Corynebacterium glutamicum in complex with D,L-diaminopimelate | |||||||||
Components | Diaminopimelate epimerase | |||||||||
Keywords | ISOMERASE | |||||||||
Function / homology | Function and homology information diaminopimelate epimerase / diaminopimelate epimerase activity / lysine biosynthetic process via diaminopimelate / cytosol Similarity search - Function | |||||||||
Biological species | Corynebacterium glutamicum (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å | |||||||||
Authors | Sagong, H.-Y. / Kim, K.-J. | |||||||||
Citation | Journal: Sci Rep / Year: 2017 Title: Structural basis for redox sensitivity in Corynebacterium glutamicum diaminopimelate epimerase: an enzyme involved in l-lysine biosynthesis. Authors: Sagong, H.Y. / Kim, K.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5m47.cif.gz | 67 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m47.ent.gz | 49.4 KB | Display | PDB format |
PDBx/mmJSON format | 5m47.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5m47_validation.pdf.gz | 446.6 KB | Display | wwPDB validaton report |
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Full document | 5m47_full_validation.pdf.gz | 450.4 KB | Display | |
Data in XML | 5m47_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 5m47_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m4/5m47 ftp://data.pdbj.org/pub/pdb/validation_reports/m4/5m47 | HTTPS FTP |
-Related structure data
Related structure data | 5h2gC 5h2ySC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30054.732 Da / Num. of mol.: 1 / Fragment: Epimerase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025) (bacteria) Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025 Gene: dapF, Cgl1943, cg2129 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8NP73, diaminopimelate epimerase |
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#2: Chemical | ChemComp-API / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.3 Å3/Da / Density % sol: 76.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: Sodium citrate, CHES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 15, 2015 |
Radiation | Monochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→110.1 Å / Num. obs: 19071 / % possible obs: 97.4 % / Redundancy: 12 % / Rmerge(I) obs: 0.115 / Rsym value: 0.344 / Net I/σ(I): 21.1 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 4 / % possible all: 93.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5H2Y Resolution: 2.59→110.09 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.91 / SU B: 8.502 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.231 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 113.57 Å2 / Biso mean: 34.446 Å2 / Biso min: 8.97 Å2
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Refinement step | Cycle: final / Resolution: 2.59→110.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.594→2.662 Å / Total num. of bins used: 20
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