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Yorodumi- PDB-3n4i: Crystal structure of the SHV-1 D104E beta-lactamase/beta-lactamas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3n4i | ||||||
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Title | Crystal structure of the SHV-1 D104E beta-lactamase/beta-lactamase inhibitor protein (BLIP) complex | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / beta-lactamase / protein-protein complex / BLIP / SHV-1 / HYDROLASE - HYDROLASE INHIBITOR complex / 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 / molecular replacement / Resolution: 1.56 Å | ||||||
Authors | Hanes, M.S. / Reynolds, K.A. / McNamara, C. / Ghosh, P. / Bonomo, R.A. / Kirsch, J.F. / Handel, T.M. | ||||||
Citation | Journal: Proteins / Year: 2011 Title: Specificity and Cooperativity at beta-lactamase Position 104 in TEM-1/BLIP and SHV-1/BLIP interactions Authors: Hanes, M.S. / Reynolds, K.A. / McNamara, C. / Ghosh, P. / Bonomo, R.A. / Kirsch, J.F. / 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 | 3n4i.cif.gz | 102.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n4i.ent.gz | 76.9 KB | Display | PDB format |
PDBx/mmJSON format | 3n4i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3n4i_validation.pdf.gz | 427.4 KB | Display | wwPDB validaton report |
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Full document | 3n4i_full_validation.pdf.gz | 429.7 KB | Display | |
Data in XML | 3n4i_validation.xml.gz | 20.2 KB | Display | |
Data in CIF | 3n4i_validation.cif.gz | 30.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n4/3n4i ftp://data.pdbj.org/pub/pdb/validation_reports/n4/3n4i | HTTPS FTP |
-Related structure data
Related structure data | 2g2uS 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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-Components
#1: Protein | Mass: 28921.045 Da / Num. of mol.: 1 / Mutation: D104E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bla, bla SHV1, RSMK03643, RSMK03800, shv1 / Plasmid: pBCSK(-) / Production host: Escherichia coli (E. coli) / Strain (production host): DH10B / 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) / Gene: bli / Plasmid: pET26b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P35804 |
#3: 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: 3.71 Å3/Da / Density % sol: 66.89 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 40% ammonium sulfate, 100mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.1159 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 3, 2006 |
Radiation | Monochromator: 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: 1.56→36.9 Å / Num. all: 96515 / Num. obs: 96164 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Rmerge(I) obs: 0.082 / Χ2: 0.992 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.56→1.62 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.447 / Num. unique all: 9313 / Χ2: 1.009 / % possible all: 96.8 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 0.362 / Cor.coef. Fo:Fc: 0.666 / Cor.coef. Io to Ic: 0.578
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2G2U Resolution: 1.56→36.9 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.965 / WRfactor Rfree: 0.203 / WRfactor Rwork: 0.189 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.896 / SU B: 0.975 / SU ML: 0.036 / SU R Cruickshank DPI: 0.059 / SU Rfree: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.057 / 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 max: 102.87 Å2 / Biso mean: 20.907 Å2 / Biso min: 8.45 Å2
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Refinement step | Cycle: LAST / Resolution: 1.56→36.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.56→1.602 Å / Total num. of bins used: 20
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