+Open data
-Basic information
Entry | Database: PDB / ID: 1tdg | ||||||
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Title | Complex of S130G SHV-1 beta-lactamase with tazobactam | ||||||
Components | Beta-lactamase SHV-1 | ||||||
Keywords | HYDROLASE / S130G SHV-1 class A beta-lactamase / penicillinase / beta-lactam hydrolase / detergent binding / inhibitor complex / tazobactam / aldehyde / cymal-6 | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Sun, T. / Bethel, C.R. / Bonomo, R.A. / Knox, J.R. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Inhibitor-resistant class A beta-lactamases: consequences of the Ser130-to-Gly mutation seen in Apo and tazobactam structures of the SHV-1 variant Authors: Sun, T. / Bethel, C.R. / Bonomo, R.A. / Knox, J.R. | ||||||
History |
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Remark 600 | HETEROGEN Apparent short contacts between the 2 intermediates, TBE and MDD, arise because the ...HETEROGEN Apparent short contacts between the 2 intermediates, TBE and MDD, arise because the crystal structure contains a composite of 2 complexes, one a breakdown product of the other. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tdg.cif.gz | 82.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tdg.ent.gz | 59.7 KB | Display | PDB format |
PDBx/mmJSON format | 1tdg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tdg_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 1tdg_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 1tdg_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 1tdg_validation.cif.gz | 27.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/td/1tdg ftp://data.pdbj.org/pub/pdb/validation_reports/td/1tdg | HTTPS FTP |
-Related structure data
Related structure data | 1tdlC 1shvS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 28876.994 Da / Num. of mol.: 1 / Mutation: S130G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla / Plasmid: pBC SK / Species (production host): Escherichia coli Production host: Escherichia coli str. K-12 substr. DH10B (bacteria) Strain (production host): DH10B References: UniProt: P14557, UniProt: P0AD64*PLUS, beta-lactamase |
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-Non-polymers , 6 types, 402 molecules
#2: Chemical | #3: Chemical | ChemComp-TBE / | #4: Chemical | ChemComp-MDD / | #5: Chemical | ChemComp-MRD / ( | #6: Chemical | ChemComp-MPD / ( | #7: 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: 1.99 Å3/Da / Density % sol: 38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 15% PEG 6000, 50 mM HEPES, 0.56 mM Cymal-6 detergent, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Jul 1, 2003 / Details: double-mirror Franks focusing |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→28 Å / Num. all: 22043 / Num. obs: 20318 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.8→1.91 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.138 / Mean I/σ(I) obs: 4.5 / Num. unique all: 3624 / Rsym value: 0.138 / % possible all: 79.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SHV Resolution: 1.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: Atoms having alternate conformations are only listed once in the above list of the number of atoms used in the refinement
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Displacement parameters | Biso mean: 10.9 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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LS refinement shell |
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