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Yorodumi- PDB-5npo: Promiscuous Protein Self-Assembly as a Function of Protein Stability -
+Open data
-Basic information
Entry | Database: PDB / ID: 5npo | ||||||
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Title | Promiscuous Protein Self-Assembly as a Function of Protein Stability | ||||||
Components |
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Keywords | HYDROLASE / TEM1 beta-lactamase Hetrodimer | ||||||
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 coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Cohen-Khait, R. / Dym, O. / Hamer-Rogotner, S. / Schreiber, G. | ||||||
Citation | Journal: Structure / Year: 2017 Title: Promiscuous Protein Binding as a Function of Protein Stability. Authors: Cohen-Khait, R. / Dym, O. / Hamer-Rogotner, S. / Schreiber, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5npo.cif.gz | 107 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5npo.ent.gz | 80.3 KB | Display | PDB format |
PDBx/mmJSON format | 5npo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5npo_validation.pdf.gz | 440.6 KB | Display | wwPDB validaton report |
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Full document | 5npo_full_validation.pdf.gz | 443.2 KB | Display | |
Data in XML | 5npo_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 5npo_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/np/5npo ftp://data.pdbj.org/pub/pdb/validation_reports/np/5npo | HTTPS FTP |
-Related structure data
Related structure data | 4op5S 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: 29087.217 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla, blaT-3, blaT-4, blaT-5, blaT-6 / Production host: Escherichia coli (E. coli) / References: UniProt: P62593, beta-lactamase |
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#2: Protein | Mass: 28955.143 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: D3INY1, beta-lactamase |
#3: Chemical | ChemComp-MG / |
#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: 2.24 Å3/Da / Density % sol: 44.97 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 7.5% PEG 6000, 0.1M MgCl2 and 0.05M Sodium acetate pH=5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Feb 15, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→67.94 Å / Num. obs: 34416 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rsym value: 0.069 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1696 / Rsym value: 0.67 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4op5 Resolution: 1.95→67.94 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.505 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.172 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.068 Å2
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Refinement step | Cycle: 1 / Resolution: 1.95→67.94 Å
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Refine LS restraints |
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