+Open data
-Basic information
Entry | Database: PDB / ID: 6n9k | |||||||||
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Title | Beta-lactamase from Escherichia coli str. Sakai | |||||||||
Components | Beta-lactamase | |||||||||
Keywords | LIGASE / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID | |||||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic Similarity search - Function | |||||||||
Biological species | Escherichia coli O157:H7 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | |||||||||
Authors | Osipiuk, J. / Wu, R. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | |||||||||
Funding support | United States, 2items
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Citation | Journal: to be published Title: Beta-lactamase from Escherichia coli str. Sakai Authors: Osipiuk, J. / Wu, R. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6n9k.cif.gz | 309.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6n9k.ent.gz | 250.7 KB | Display | PDB format |
PDBx/mmJSON format | 6n9k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6n9k_validation.pdf.gz | 466.2 KB | Display | wwPDB validaton report |
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Full document | 6n9k_full_validation.pdf.gz | 468 KB | Display | |
Data in XML | 6n9k_validation.xml.gz | 33.8 KB | Display | |
Data in CIF | 6n9k_validation.cif.gz | 51.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n9/6n9k ftp://data.pdbj.org/pub/pdb/validation_reports/n9/6n9k | HTTPS FTP |
-Related structure data
Related structure data | 5ggwS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-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: 39852.207 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Strain: Sakai / Gene: ampC, ECpv15279_5067, ECs_5131 / Plasmid: pMCSG53 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q8XDQ2, beta-lactamase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / #5: 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: 2.76 Å3/Da / Density % sol: 55.48 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.2 M Lithium Sulfate, 30% PEG 8000, 0.1 M Sodium Acetate:Acetic Acid buffer |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 19, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→47.64 Å / Num. obs: 112960 / % possible obs: 99.7 % / Redundancy: 9 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.021 / Rrim(I) all: 0.066 / Χ2: 1.223 / Net I/av σ(I): 34.3 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.54 / Num. unique obs: 5360 / CC1/2: 0.687 / Rpim(I) all: 0.337 / Rrim(I) all: 0.701 / Χ2: 0.619 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5GGW Resolution: 1.6→47.64 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.971 / SU B: 2.437 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.063 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 73.31 Å2 / Biso mean: 20.122 Å2 / Biso min: 11.84 Å2
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Refinement step | Cycle: final / Resolution: 1.6→47.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.602→1.644 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | S11: 0.0162 Å ° / T33: 0.0017 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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