+Open data
-Basic information
Entry | Database: PDB / ID: 5wck | |||||||||
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Title | Native FEZ-1 metallo-beta-lactamase from Legionella gormanii | |||||||||
Components | FEZ-1 protein | |||||||||
Keywords | HYDROLASE | |||||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / metal ion binding Similarity search - Function | |||||||||
Biological species | Fluoribacter gormanii (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.65 Å | |||||||||
Authors | Garcia-Saez, I. / Mercuri, P.S. / Kahn, R. / Papamicael, C. / Shabalin, I.G. / Raczynska, J.E. / Jaskolski, M. / Minor, W. / Frere, J.M. / Galleni, M. / Dideberg, O. | |||||||||
Citation | Journal: J. Mol. Biol. / Year: 2003 Title: Three-dimensional structure of FEZ-1, a monomeric subclass B3 metallo-beta-lactamase from Fluoribacter gormanii, in native form and in complex with D-captopril. Authors: Garcia-Saez, I. / Mercuri, P.S. / Papamicael, C. / Kahn, R. / Frere, J.M. / Galleni, M. / Rossolini, G.M. / Dideberg, O. #1: Journal: Drug Resist. Updat. / Year: 2018 Title: A close look onto structural models and primary ligands of metallo-beta-lactamases. Authors: Raczynska, J.E. / Shabalin, I.G. / Minor, W. / Wlodawer, A. / Jaskolski, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wck.cif.gz | 141.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wck.ent.gz | 106.8 KB | Display | PDB format |
PDBx/mmJSON format | 5wck.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wck_validation.pdf.gz | 455.2 KB | Display | wwPDB validaton report |
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Full document | 5wck_full_validation.pdf.gz | 455.9 KB | Display | |
Data in XML | 5wck_validation.xml.gz | 29.5 KB | Display | |
Data in CIF | 5wck_validation.cif.gz | 47 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wc/5wck ftp://data.pdbj.org/pub/pdb/validation_reports/wc/5wck | HTTPS FTP |
-Related structure data
Related structure data | 1jt1C 1k07SC 1l9yC 5w90C 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 20 - 282 / Label seq-ID: 1 - 263
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 29316.463 Da / Num. of mol.: 2 / Fragment: residues 20-282 / Mutation: Q248S, A282G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fluoribacter gormanii (bacteria) / Gene: blaFEZ-1, Lgor_2502 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)(PLYSS) / References: UniProt: Q9K578, beta-lactamase |
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-Non-polymers , 5 types, 885 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | ChemComp-UNX / #6: 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: 2.27 Å3/Da / Density % sol: 45.9 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 1K07. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 20% PEG4000, 0.2M ammonium sulfate, 0.010MM ZnCl2, pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 29, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. obs: 61308 / % possible obs: 97.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.029 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 1.65→1.74 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.051 / Num. unique obs: 8838 / Rsym value: 0.037 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1K07 Resolution: 1.65→24.93 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.1687 / WRfactor Rwork: 0.1319 / FOM work R set: 0.9046 / SU B: 1.175 / SU ML: 0.041 / SU R Cruickshank DPI: 0.0814 / SU Rfree: 0.0829 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.083 / 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: 94.03 Å2 / Biso mean: 13.134 Å2 / Biso min: 3.65 Å2
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Refinement step | Cycle: final / Resolution: 1.65→24.93 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 8757 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.04 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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