+Open data
-Basic information
Entry | Database: PDB / ID: 4mez | ||||||
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Title | Crystal structure of M68L/M69T double mutant TEM-1 | ||||||
Components | Beta-lactamase TEM | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.047 Å | ||||||
Authors | Park, J. / Gobeil, S. / Pelletier, J.N. / Berghuis, A.M. | ||||||
Citation | Journal: Sci Rep / Year: 2019 Title: The Structural Dynamics of Engineered beta-Lactamases Vary Broadly on Three Timescales yet Sustain Native Function. Authors: Gobeil, S.M.C. / Ebert, M.C.C.J.C. / Park, J. / Gagne, D. / Doucet, N. / Berghuis, A.M. / Pleiss, J. / Pelletier, J.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mez.cif.gz | 120.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mez.ent.gz | 92.2 KB | Display | PDB format |
PDBx/mmJSON format | 4mez.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mez_validation.pdf.gz | 444.9 KB | Display | wwPDB validaton report |
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Full document | 4mez_full_validation.pdf.gz | 447.9 KB | Display | |
Data in XML | 4mez_validation.xml.gz | 24.1 KB | Display | |
Data in CIF | 4mez_validation.cif.gz | 35.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/me/4mez ftp://data.pdbj.org/pub/pdb/validation_reports/me/4mez | HTTPS FTP |
-Related structure data
Related structure data | 4r4rC 4r4sC 1zg4S 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 oper:
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-Components
#1: Protein | Mass: 28893.865 Da / Num. of mol.: 2 / Mutation: M66L, M67T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla, blaT-3, blaT-4, blaT-5, blaT-6 / Production host: Escherichia coli (E. coli) / References: UniProt: P62593, beta-lactamase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: 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: 2.28 Å3/Da / Density % sol: 45.99 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.5M ammonium sulfate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 10, 2012 / Details: VariMax HF |
Radiation | Monochromator: VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.047→73.26 Å / Num. all: 31963 / Num. obs: 31707 / % possible obs: 99.2 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.152 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.047→2.09 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 3.5 / Num. unique all: 1521 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ZG4 Resolution: 2.047→73.26 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.887 / SU B: 4.603 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.241 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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 mean: 11.363 Å2
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Refinement step | Cycle: LAST / Resolution: 2.047→73.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.047→2.1 Å / Total num. of bins used: 20
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