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Yorodumi- PDB-1nxy: Crystal Structure of the complex between M182T mutant of TEM-1 an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nxy | ||||||
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Title | Crystal Structure of the complex between M182T mutant of TEM-1 and a boronic acid inhibitor (SM2) | ||||||
Components | Beta-lactamase TEM | ||||||
Keywords | HYDROLASE / Antibiotic resistance / beta-lactamase / deacylation transition-state analog | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Wang, X. / Minasov, G. / Blazquez, J. / Caselli, E. / Prati, F. / Shoichet, B.K. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Recognition and Resistance in TEM beta-lactamase Authors: Wang, X. / Minasov, G. / Blazquez, J. / Caselli, E. / Prati, F. / Shoichet, B.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nxy.cif.gz | 85.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nxy.ent.gz | 63.4 KB | Display | PDB format |
PDBx/mmJSON format | 1nxy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nxy_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1nxy_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1nxy_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 1nxy_validation.cif.gz | 29.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nx/1nxy ftp://data.pdbj.org/pub/pdb/validation_reports/nx/1nxy | HTTPS FTP |
-Related structure data
Related structure data | 1ny0C 1nymC 1nyyC 1jwpS 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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Unit cell |
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-Components
#1: Protein | Mass: 28911.904 Da / Num. of mol.: 1 / Mutation: M182T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla / Plasmid: pAlter EX II-TEM-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P62593, beta-lactamase | ||
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#2: Chemical | ChemComp-K / | ||
#3: Chemical | #4: 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: 2.32 Å3/Da / Density % sol: 46.94 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: sodium-potassium buffer, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||
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: APS / Beamline: 5ID-B / Wavelength: 0.98012 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 4, 2001 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98012 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→15 Å / Num. all: 36330 / Num. obs: 36330 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 29.8 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.241 / Mean I/σ(I) obs: 7.2 / Num. unique all: 3568 / % possible all: 99.5 |
Reflection | *PLUS Num. measured all: 220946 |
Reflection shell | *PLUS % possible obs: 99.5 % / Num. unique obs: 3568 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JWP Resolution: 1.6→15 Å Isotropic thermal model: Isotropic, individual B values refined Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: Maximum likelihood target for amplitudes was used in refinement
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Displacement parameters | Biso mean: 15.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.66 Å
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 10 % / Rfactor Rfree: 0.198 / Rfactor Rwork: 0.177 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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