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Yorodumi- PDB-3gmx: Crystal Structure of Beta-Lactamse Inhibitory Protein-Like Protei... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gmx | ||||||
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Title | Crystal Structure of Beta-Lactamse Inhibitory Protein-Like Protein (BLP) at 1.05 Angstrom Resolution | ||||||
Components | BLP | ||||||
Keywords | PROTEIN BINDING / 2-layer alpha/beta sandwich | ||||||
Function / homology | Function and homology information BLIP domain / Beta-lactamase-inhibitor protein BLIP / Beta-lactamase-inhibitor protein BLIP domain superfamily / Beta-lactamase inhibitor (BLIP) / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Streptomyces clavuligerus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.05 Å | ||||||
Authors | 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 | 3gmx.cif.gz | 169.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gmx.ent.gz | 141.1 KB | Display | PDB format |
PDBx/mmJSON format | 3gmx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gmx_validation.pdf.gz | 440.5 KB | Display | wwPDB validaton report |
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Full document | 3gmx_full_validation.pdf.gz | 443.3 KB | Display | |
Data in XML | 3gmx_validation.xml.gz | 22.8 KB | Display | |
Data in CIF | 3gmx_validation.cif.gz | 36.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/3gmx ftp://data.pdbj.org/pub/pdb/validation_reports/gm/3gmx | HTTPS FTP |
-Related 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: 17552.623 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces clavuligerus (bacteria) / Strain: ATCC 27064 / Gene: blp / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P97062, UniProt: B5GLC0*PLUS #2: Chemical | ChemComp-ACT / #3: 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: 2.08 Å3/Da / Density % sol: 40.84 % |
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Crystal grow | Temperature: 294 K / Method: microbatch under oil / pH: 6.5 Details: starting concentration as follows: 5.5 mg/ml protein, 10% PEG 8000, 0.1 M magnesium acetate tetrahydrate, 50 mM sodium cacodylate, 75 mM NaCl, 15 mM tris, pH 6.5, microbatch under oil, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11588 Å |
Detector | Type: ADSC QUANTUM Q315r / Detector: CCD / Date: Feb 28, 2006 |
Radiation | Monochromator: DOUBLE FLAT CRYSTAL SILICON (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11588 Å / Relative weight: 1 |
Reflection | Resolution: 1.05→49.94 Å / Num. obs: 114297 / % possible obs: 86.1 % / Redundancy: 9.9 % / Rsym value: 0.06 / Χ2: 0.997 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 1.05→1.077 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 2.3 / Num. unique all: 5662 / Χ2: 1.084 / % possible all: 65.9 |
-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.05→49.9 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.969 / Occupancy max: 1 / Occupancy min: 0 / SU B: 0.687 / SU ML: 0.016 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.03 / ESU R Free: 0.031 / 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: 57.16 Å2 / Biso mean: 11.089 Å2 / Biso min: 2.14 Å2
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Refinement step | Cycle: LAST / Resolution: 1.05→49.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.05→1.077 Å / Total num. of bins used: 20
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