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Yorodumi- PDB-2g2w: Crystal Structure of the SHV D104K Beta-lactamase/Beta-lactamase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2g2w | ||||||
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Title | Crystal Structure of the SHV D104K Beta-lactamase/Beta-lactamase inhibitor protein (BLIP) complex | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / beta-lactamase / beta-lactamase inhibitor / protein-protein complex / BLIP / SHV / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information regulation of beta-lactamase activity / beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / extracellular region Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae (bacteria) Streptomyces clavuligerus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Reynolds, K.A. / Thomson, J.M. / Corbett, K.D. / Bethel, C.R. / Berger, J.M. / Kirsch, J.F. / Bonomo, R.A. / Handel, T.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Structural and Computational Characterization of the SHV-1 beta-Lactamase-beta-Lactamase Inhibitor Protein Interface. Authors: Reynolds, K.A. / Thomson, J.M. / Corbett, K.D. / Bethel, C.R. / Berger, J.M. / Kirsch, J.F. / Bonomo, R.A. / Handel, T.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2g2w.cif.gz | 98.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2g2w.ent.gz | 72.9 KB | Display | PDB format |
PDBx/mmJSON format | 2g2w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2g2w_validation.pdf.gz | 431.2 KB | Display | wwPDB validaton report |
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Full document | 2g2w_full_validation.pdf.gz | 434.3 KB | Display | |
Data in XML | 2g2w_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | 2g2w_validation.cif.gz | 26.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/2g2w ftp://data.pdbj.org/pub/pdb/validation_reports/g2/2g2w | HTTPS FTP |
-Related structure data
Related structure data | 2g2uC 1jtgS 1shvS C: citing same article (ref.) S: Starting model for refinement |
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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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Details | The biological assembly is the complex between chain A (SHV D104K) and chain B (BLIP) |
-Components
#1: Protein | Mass: 28921.111 Da / Num. of mol.: 1 / Mutation: D104K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: Bla, shv1 / Plasmid: pET24a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0AD64, beta-lactamase |
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#2: Protein | Mass: 17556.492 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces clavuligerus (bacteria) / Plasmid: pET26b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P35804 |
#3: Water | ChemComp-HOH / |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.03 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 6.5 Details: 4% PEG 8000, 25mM cacodylate, 10 mM BisTris, 25mM NaCl, pH 6.5, EVAPORATION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 19, 2005 |
Radiation | Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1159 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 35776 / Num. obs: 35776 / % possible obs: 95.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2 % / Rsym value: 0.03 / Net I/σ(I): 25.389 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 6.07 / Rsym value: 0.096 / % possible all: 89.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: polyalanine models of chain A from PDB 1SHV and chain B from PDB 1JTG Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.158 / SU ML: 0.081 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.821 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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