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Open data
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Basic information
Entry | Database: PDB / ID: 6l4l | |||||||||
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Title | Crystal structure of S. aureus CntK in inactive state | |||||||||
![]() | Diaminopimelate epimerase | |||||||||
![]() | ISOMERASE / disulfide / racemase | |||||||||
Function / homology | histidine racemase / isomerase activity / Histidine racemase / Diaminopimelate epimerase![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ju, Y. / Luo, S. / Zhou, H. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of S. aureus CntK in inactive state Authors: Ju, Y. / Luo, S. / Zhou, H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 66.9 KB | Display | ![]() |
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PDB format | ![]() | 46.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6jisS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 32109.197 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 46.06 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.05 M HEPES pH7.5, 26% PEG 400 / PH range: 7.3-7.7 |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Dec 28, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 19154 / % possible obs: 98 % / Redundancy: 3.3 % / Rrim(I) all: 0.072 / Net I/σ(I): 20.646 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.501 / Num. unique obs: 1897 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6JIS Resolution: 2→30.16 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.62 / SU ML: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.16 / 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: 82.54 Å2 / Biso mean: 36.799 Å2 / Biso min: 23.19 Å2
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Refinement step | Cycle: final / Resolution: 2→30.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.002→2.054 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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