+Open data
-Basic information
Entry | Database: PDB / ID: 1k07 | ||||||
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Title | Native FEZ-1 metallo-beta-lactamase from Legionella gormanii | ||||||
Components | FEZ-1 beta-lactamase | ||||||
Keywords | HYDROLASE / monomer with alpha-beta/beta-alpha fold. Two monomers per assymmetric unit. | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Garcia-Saez, I. / Mercuri, P.S. / Kahn, R. / Papamicael, C. / 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 -Captopril Authors: Garcia-Saez, I. / Mercuri, P.S. / Papamicael, C. / Kahn, R. / Frere, J.M. / Galleni, M. / Rossolini, G.M. / Dideberg, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k07.cif.gz | 129.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k07.ent.gz | 98.9 KB | Display | PDB format |
PDBx/mmJSON format | 1k07.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1k07_validation.pdf.gz | 478.7 KB | Display | wwPDB validaton report |
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Full document | 1k07_full_validation.pdf.gz | 482.4 KB | Display | |
Data in XML | 1k07_validation.xml.gz | 26.7 KB | Display | |
Data in CIF | 1k07_validation.cif.gz | 39.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k0/1k07 ftp://data.pdbj.org/pub/pdb/validation_reports/k0/1k07 | HTTPS FTP |
-Related structure data
Related structure data | 1jt1SC 1l9yC 5w90C 5wckC 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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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 29316.463 Da / Num. of mol.: 2 / Fragment: RESIDUES 20-282 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fluoribacter gormanii (bacteria) / Gene: blaFEZ-1 / Plasmid: pDML1810 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)(pLysS) / References: UniProt: Q9K578, beta-lactamase |
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-Non-polymers , 5 types, 514 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | ChemComp-GOL / #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: 45.74 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 20% PEG4000, 0.2M ammonium sulfate, 0.010MM ZnCl2, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 6 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9 Å |
Detector | 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→25 Å / Num. all: 61458 / Num. obs: 61308 / % possible obs: 97.9 % / Observed criterion σ(I): 3 / Redundancy: 3.5 % / Biso Wilson estimate: 10.775 Å2 / Rmerge(I) obs: 0.029 / Rsym value: 0.021 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 1.65→1.74 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.051 / Num. unique all: 8838 / Rsym value: 0.037 / % possible all: 96.9 |
Reflection | *PLUS Lowest resolution: 25 Å / Num. obs: 61458 / Num. measured all: 217456 / Rmerge(I) obs: 0.021 |
Reflection shell | *PLUS % possible obs: 96.9 % / Rmerge(I) obs: 0.037 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JT1 Resolution: 1.65→25 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 Details: Refinement of double conformation of residues 221 and 255 in A and B chains (two monomers per assym/unit), double conformation of hetero-atoms 502A and 503B and two different positions for waters 127 and 178.
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→25 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement | *PLUS Lowest resolution: 25 Å / % reflection Rfree: 10 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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