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Yorodumi- PDB-6knt: Crystal structure of the metallo-beta-lactamase fold protein YhfI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6knt | ||||||
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Title | Crystal structure of the metallo-beta-lactamase fold protein YhfI from Bacillus subtilis (space group P4332) | ||||||
Components | Putative metal-dependent hydrolase | ||||||
Keywords | HYDROLASE / enzyme / metallo-beta-lactamase fold protein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Na, H.W. / Namgung, B. / Song, W.S. / Yoon, S.I. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2019 Title: Structural and biochemical analyses of the metallo-beta-lactamase fold protein YhfI from Bacillus subtilis. Authors: Na, H.W. / Namgung, B. / Song, W.S. / Yoon, S.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6knt.cif.gz | 381.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6knt.ent.gz | 313.3 KB | Display | PDB format |
PDBx/mmJSON format | 6knt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kn/6knt ftp://data.pdbj.org/pub/pdb/validation_reports/kn/6knt | HTTPS FTP |
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-Related structure data
Related structure data | 6knsSC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 27081.355 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yhfI / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: E0TYN8 #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 3.26 Å3/Da / Density % sol: 62.26 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: ammonium sulfate, Hepes |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 27, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 49583 / % possible obs: 99.8 % / Redundancy: 8 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 30.8 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 4.5 / Num. unique obs: 4859 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 6KNS Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / SU B: 13.774 / SU ML: 0.157 / Cross valid method: FREE R-VALUE / ESU R: 0.328 / ESU R Free: 0.234 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 122.28 Å2 / Biso mean: 44.73 Å2 / Biso min: 17.08 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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