+Open data
-Basic information
Entry | Database: PDB / ID: 6sar | ||||||
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Title | E coli BepA/YfgC | ||||||
Components | Beta-barrel assembly-enhancing protease | ||||||
Keywords | CHAPERONE / outer membrane bam complex chaperone protease | ||||||
Function / homology | Function and homology information Gram-negative-bacterium-type cell outer membrane assembly / Hydrolases; Acting on peptide bonds (peptidases) / protein disulfide isomerase activity / chaperone-mediated protein folding / proteolysis involved in protein catabolic process / metalloendopeptidase activity / outer membrane-bounded periplasmic space / zinc ion binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.18 Å | ||||||
Authors | Lovering, A.L. / Cadby, I.T. | ||||||
Citation | Journal: J.Bacteriol. / Year: 2020 Title: Structure-Function Characterization of the Conserved Regulatory Mechanism of the Escherichia coli M48 Metalloprotease BepA. Authors: Bryant, J.A. / Cadby, I.T. / Chong, Z.S. / Boelter, G. / Sevastsyanovich, Y.R. / Morris, F.C. / Cunningham, A.F. / Kritikos, G. / Meek, R.W. / Banzhaf, M. / Chng, S.S. / Lovering, A.L. / Henderson, I.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6sar.cif.gz | 171.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sar.ent.gz | 135.7 KB | Display | PDB format |
PDBx/mmJSON format | 6sar.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6sar_validation.pdf.gz | 431.6 KB | Display | wwPDB validaton report |
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Full document | 6sar_full_validation.pdf.gz | 431.9 KB | Display | |
Data in XML | 6sar_validation.xml.gz | 16 KB | Display | |
Data in CIF | 6sar_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sa/6sar ftp://data.pdbj.org/pub/pdb/validation_reports/sa/6sar | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 53962.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: bepA, yfgC, b2494, JW2479 / Production host: Escherichia coli (E. coli) References: UniProt: P66948, Hydrolases; Acting on peptide bonds (peptidases) |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.92 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M Na HEPES, pH 7.0, and 8% w/v PEG 8,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.28274 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 1, 2015 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.28274 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.18→77.02 Å / Num. obs: 27140 / % possible obs: 98.9 % / Redundancy: 16.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.028 / Rrim(I) all: 0.119 / Net I/σ(I): 20.8 / Num. measured all: 448076 / Scaling rejects: 467 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.18→77.02 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.955 / SU B: 9.6 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.199 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 116.01 Å2 / Biso mean: 47.398 Å2 / Biso min: 24.94 Å2
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Refinement step | Cycle: final / Resolution: 2.18→77.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.18→2.237 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 29.966 Å / Origin y: 48.42 Å / Origin z: 44.623 Å
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