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Yorodumi- PDB-3gmu: Crystal Structure of Beta-Lactamse Inhibitory Protein (BLIP) in A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gmu | ||||||
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Title | Crystal Structure of Beta-Lactamse Inhibitory Protein (BLIP) in Apo Form | ||||||
Components | Beta-lactamase inhibitory proteinBeta-lactamase inhibitor protein | ||||||
Keywords | PROTEIN BINDING / 2-layer alpha/beta sandwich / Disulfide bond / Secreted | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces clavuligerus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.98 Å | ||||||
Authors | Strynadka, N.C.J. / Gretes, M. / James, M.N.G. | ||||||
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. #1: Journal: Nature / Year: 1994 Title: Structural and kinetic characterization of a beta-lactamase-inhibitor protein. Authors: Strynadka, N.C. / Jensen, S.E. / Johns, K. / Blanchard, H. / Page, M. / Matagne, A. / Frere, J.M. / James, M.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gmu.cif.gz | 42.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gmu.ent.gz | 32.7 KB | Display | PDB format |
PDBx/mmJSON format | 3gmu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/3gmu ftp://data.pdbj.org/pub/pdb/validation_reports/gm/3gmu | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 17556.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell culture filtrate / Source: (natural) Streptomyces clavuligerus (bacteria) / Strain: NRRL 3585 / References: UniProt: P35804 |
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#2: Chemical | ChemComp-NH4 / |
#3: Chemical | ChemComp-SO4 / |
#4: 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: 2.13 Å3/Da / Density % sol: 42.15 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 5.5 Details: 10 mg/ml protein, 20% saturated ammonium sulfate, 50 mM sodium citrate, pH 5.5, vapor diffusion, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54056 Å |
Detector | Type: SDMS TWIN AREA DETECTOR SYSTEM / Detector: AREA DETECTOR / Date: Dec 17, 1992 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54056 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→59.34 Å / Num. obs: 9038 / % possible obs: 84.6 % / Redundancy: 1.9 % / Rsym value: 0.178 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 1.98→2.03 Å / Mean I/σ(I) obs: 1.8 / % possible all: 64.8 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→59.3 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.911 / WRfactor Rfree: 0.221 / WRfactor Rwork: 0.149 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.863 / SU B: 3.915 / SU ML: 0.115 / SU R Cruickshank DPI: 0.228 / SU Rfree: 0.193 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / ESU R Free: 0.193 / 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: 56.93 Å2 / Biso mean: 18.946 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→59.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.98→2.03 Å / Total num. of bins used: 20
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