+Open data
-Basic information
Entry | Database: PDB / ID: 3s4x | ||||||
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Title | Crystal structure of the Asn152Gly mutant of P99 beta-lactamase | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE / cephalosporinase | ||||||
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 | Enterobacter cloacae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Ruble, J.F. / Powers, R.A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Structural analysis of the Asn152Gly mutant of P99 cephalosporinase. Authors: Ruble, J.F. / Lefurgy, S.T. / Cornish, V.W. / Powers, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3s4x.cif.gz | 88.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3s4x.ent.gz | 65.9 KB | Display | PDB format |
PDBx/mmJSON format | 3s4x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3s4x_validation.pdf.gz | 438.5 KB | Display | wwPDB validaton report |
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Full document | 3s4x_full_validation.pdf.gz | 439.7 KB | Display | |
Data in XML | 3s4x_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | 3s4x_validation.cif.gz | 24.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s4/3s4x ftp://data.pdbj.org/pub/pdb/validation_reports/s4/3s4x | HTTPS FTP |
-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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 40081.637 Da / Num. of mol.: 1 / Mutation: I16V, A88P, N152G, A299V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter cloacae (bacteria) / Strain: P99 / Gene: ampC / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P05364, beta-lactamase | ||
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#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.46 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.15 M ammonium sulfate, 30% polyethylene glycol (PEG) 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 14, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 25774 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.104 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.95→2.02 Å / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1XX2 Resolution: 1.95→35 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.685 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.865 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→1.997 Å / Total num. of bins used: 20
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