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Yorodumi- PDB-1yms: X-ray crystallographic structure of CTX-M-9 beta-lactamase comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yms | ||||||
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Title | X-ray crystallographic structure of CTX-M-9 beta-lactamase complexed with nafcinin-like boronic acid inhibitor | ||||||
Components | beta-lactamase CTX-M-9 | ||||||
Keywords | HYDROLASE / CTX-M / beta-lactamase / transition state / acylation | ||||||
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 | Chen, Y. / Shoichet, B. / Bonnet, R. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2005 Title: Structure, Function, and Inhibition along the Reaction Coordinate of CTX-M beta-Lactamases. Authors: Chen, Y. / Shoichet, B. / Bonnet, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yms.cif.gz | 129.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yms.ent.gz | 98.9 KB | Display | PDB format |
PDBx/mmJSON format | 1yms.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yms_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1yms_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1yms_validation.xml.gz | 28.8 KB | Display | |
Data in CIF | 1yms_validation.cif.gz | 45.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ym/1yms ftp://data.pdbj.org/pub/pdb/validation_reports/ym/1yms | HTTPS FTP |
-Related structure data
Related structure data | 1ylyC 1ylzC 1ym1C 1ymxC 1yljS 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
#1: Protein | Mass: 27972.494 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CTX-M / Plasmid: pET-9a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Keywords: CTX-M-9 beta-lactamase, V231A / References: UniProt: Q9L5C8, beta-lactamase #2: Chemical | #3: 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: 2.02 Å3/Da / Density % sol: 38.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8 Details: potassium phosphate, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 / Wavelength: 1.11587 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 17, 2004 / Details: mirrors |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→22 Å / Num. all: 58748 / Num. obs: 57897 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.22 % / Biso Wilson estimate: 10.8 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.6→1.66 Å / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 2.48 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YLJ Resolution: 1.6→19.75 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 81987.04 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: ONLY 5 ATOMS WERE MODELED FOR A25 GLN with the side chain truncated after CB
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.3739 Å2 / ksol: 0.36281 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→19.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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