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Yorodumi- PDB-3gmw: Crystal Structure of Beta-Lactamse Inhibitory Protein-I (BLIP-I) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gmw | ||||||
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Title | Crystal Structure of Beta-Lactamse Inhibitory Protein-I (BLIP-I) in Complex with TEM-1 Beta-Lactamase | ||||||
Components |
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Keywords | PROTEIN BINDING / protein-protein complex / Antibiotic resistance / Hydrolase / Plasmid | ||||||
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 sp. Sflu5 (bacteria) Streptomyces exfoliatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å | ||||||
Authors | Lim, D.C. / Gretes, M. / Strynadka, N.C.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Insights into positive and negative requirements for protein-protein interactions by crystallographic analysis of the beta-lactamase inhibitory proteins BLIP, BLIP-I, and BLP. Authors: Gretes, M. / Lim, D.C. / de Castro, L. / Jensen, S.E. / Kang, S.G. / Lee, K.J. / Strynadka, N.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gmw.cif.gz | 174.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gmw.ent.gz | 143.6 KB | Display | PDB format |
PDBx/mmJSON format | 3gmw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gmw_validation.pdf.gz | 448.6 KB | Display | wwPDB validaton report |
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Full document | 3gmw_full_validation.pdf.gz | 478.5 KB | Display | |
Data in XML | 3gmw_validation.xml.gz | 39.1 KB | Display | |
Data in CIF | 3gmw_validation.cif.gz | 54.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/3gmw ftp://data.pdbj.org/pub/pdb/validation_reports/gm/3gmw | HTTPS FTP |
-Related 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: 28734.791 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia sp. Sflu5 (bacteria) / Strain: cb86134 / Gene: amp, bla / Plasmid: pUC118 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5PHA6 #2: Protein | Mass: 17218.963 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces exfoliatus (bacteria) / Strain: SMF19 / Gene: bliA / Plasmid: pET30a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9KJ90 #3: Chemical | ChemComp-PO4 / #4: 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: 2.49 Å3/Da / Density % sol: 50.57 % |
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Crystal grow | Temperature: 294 K / Method: hanging drop vapor batch Details: 10 mg/ml of each protein in 50 mM TrisCl, pH 8.0, 0.05 M NaCl mixed 1:1 with 0.2 M potassium phosphate, pH 4.7, 20% PEG 3350, hanging drop vapor batch, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 1, 2001 |
Radiation | Monochromator: DOUBLE CRYSTAL SILICON (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→105.41 Å / Num. obs: 49303 / % possible obs: 94.7 % / Redundancy: 5.4 % / Rsym value: 0.048 / Net I/σ(I): 14.438 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.111 / Rsym value: 0.111 / % possible all: 86.5 |
-Processing
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Refinement | Resolution: 2.1→25 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.91 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.22 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.25 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 26.319 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20
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