+Open data
-Basic information
Entry | Database: PDB / ID: 7ev5 | ||||||
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Title | Crystal structure of BLEG-1 B3 metallo-beta-lactamase | ||||||
Components | Lactamase_B domain-containing protein | ||||||
Keywords | HYDROLASE / B3 metallo-beta-lactamase / glyoxalase II / Metallo-hydrolase-like_MBL-fold protein | ||||||
Function / homology | Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / IODIDE ION / Lactamase_B domain-containing protein Function and homology information | ||||||
Biological species | Bacillus lehensis G1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.44 Å | ||||||
Authors | Au, S.X. / Muhd Noor, N.D. / Matsumura, H. / Rahman, R.N.Z.R.A. / Normi, Y.M. | ||||||
Citation | Journal: Int J Mol Sci / Year: 2021 Title: Dual Activity BLEG-1 from Bacillus lehensis G1 Revealed Structural Resemblance to B3 Metallo-beta-Lactamase and Glyoxalase II: An Insight into Its Enzyme Promiscuity and Evolutionary Divergence. Authors: Au, S.X. / Dzulkifly, N.S. / Muhd Noor, N.D. / Matsumura, H. / Raja Abdul Rahman, R.N.Z. / Normi, Y.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ev5.cif.gz | 64.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ev5.ent.gz | 43.6 KB | Display | PDB format |
PDBx/mmJSON format | 7ev5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ev5_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7ev5_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7ev5_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 7ev5_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ev/7ev5 ftp://data.pdbj.org/pub/pdb/validation_reports/ev/7ev5 | HTTPS FTP |
-Related structure data
Related structure data | 2xf4S S: Starting model for refinement |
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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: 23251.293 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus lehensis G1 (bacteria) / Plasmid: pET-28(b) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A060M4R1 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-IOD / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % / Description: Tetragonal |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: NaI, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU / Detector: CCD / Date: Jul 19, 2019 |
Radiation | Monochromator: Copper / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.44→50 Å / Num. obs: 40528 / % possible obs: 98 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 28.5 |
Reflection shell | Resolution: 1.44→1.46 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 4 / Num. unique obs: 1991 / CC1/2: 0.899 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2XF4 Resolution: 1.44→30.26 Å / Cross valid method: FREE R-VALUE / Stereochemistry target values: ML
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Solvent computation | Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.3 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.44→30.26 Å
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Refine LS restraints |
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LS refinement shell |
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