+Open data
-Basic information
Entry | Database: PDB / ID: 6kyc | ||||||
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Title | Structure of the S207A mutant of Clostridium difficile sortase B | ||||||
Components | Putative peptidase C60B, sortase B | ||||||
Keywords | HYDROLASE / sortase B / cysteine transpeptidase / Clostridium difficile | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Peptoclostridium difficile 630 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.604 Å | ||||||
Authors | Kang, C.Y. / Huang, I.H. / Wu, T.Y. / Chang, J.C. / Hsiao, Y.Y. / Cheng, C.H. / Tsai, W.J. / Hsu, K.C. / Wang, S.Y. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2020 Title: Functional analysis ofClostridium difficilesortase B reveals key residues for catalytic activity and substrate specificity. Authors: Kang, C.Y. / Huang, I.H. / Chou, C.C. / Wu, T.Y. / Chang, J.C. / Hsiao, Y.Y. / Cheng, C.H. / Tsai, W.J. / Hsu, K.C. / Wang, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kyc.cif.gz | 91.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kyc.ent.gz | 68 KB | Display | PDB format |
PDBx/mmJSON format | 6kyc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kyc_validation.pdf.gz | 420 KB | Display | wwPDB validaton report |
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Full document | 6kyc_full_validation.pdf.gz | 420 KB | Display | |
Data in XML | 6kyc_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | 6kyc_validation.cif.gz | 10.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ky/6kyc ftp://data.pdbj.org/pub/pdb/validation_reports/ky/6kyc | HTTPS FTP |
-Related structure data
Related structure data | 6kydC 5gyjS S: Starting model for refinement C: citing same article (ref.) |
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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: 26173.283 Da / Num. of mol.: 1 / Mutation: S207A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Peptoclostridium difficile 630 (bacteria) Strain: 630 / Gene: CD630_27180 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q183F3 |
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#2: 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: 2.82 Å3/Da / Density % sol: 56.35 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 4.2 / Details: 23% PEG3350, 0.1M Glycine, 0.1M citric acid(pH4.2) / PH range: 4.0-4.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 24, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→30 Å / Num. obs: 9127 / % possible obs: 99.4 % / Redundancy: 7.1 % / Biso Wilson estimate: 41.32 Å2 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.02 / Rrim(I) all: 0.056 / Χ2: 0.937 / Net I/σ(I): 15.1 / Num. measured all: 64443 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5GYJ Resolution: 2.604→28.513 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 24.49 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 98.41 Å2 / Biso mean: 44.4123 Å2 / Biso min: 16.96 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.604→28.513 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: -8.9583 Å / Origin y: -34.8259 Å / Origin z: -42.0221 Å
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Refinement TLS group |
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