+Open data
-Basic information
Entry | Database: PDB / ID: 2zc7 | ||||||
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Title | Crystal Structure of Class C beta-Lactamase ACT-1 | ||||||
Components | Beta-lactamase ACT-1 | ||||||
Keywords | HYDROLASE / two-domain structure | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Shimizu-Ibuka, A. / Sakai, H. / Galleni, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2008 Title: Structure of the plasmid-mediated class C beta-lactamase ACT-1 Authors: Shimizu-Ibuka, A. / Bauvois, C. / Sakai, H. / Galleni, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zc7.cif.gz | 282.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zc7.ent.gz | 229.9 KB | Display | PDB format |
PDBx/mmJSON format | 2zc7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zc/2zc7 ftp://data.pdbj.org/pub/pdb/validation_reports/zc/2zc7 | HTTPS FTP |
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-Related structure data
Related structure data | 1xx2S 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 39321.953 Da / Num. of mol.: 4 / Fragment: residues in database 23-381 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q48428, beta-lactamase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.81 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% PEG4000, 0.1M Tris-HCl, 0.2M sodium acetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 28, 2003 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 86460 / Num. obs: 86460 / % possible obs: 89.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 2 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 30.2 / Num. unique all: 8455 / % possible all: 84.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1XX2 Resolution: 2.4→20 Å / Isotropic thermal model: anisotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati coordinate error obs: 0.51 Å / Luzzati d res low obs: 20 Å / Luzzati sigma a obs: -0.89 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.51 Å |