+Open data
-Basic information
Entry | Database: PDB / ID: 4ux7 | ||||||
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Title | Structure of a Clostridium difficile sortase | ||||||
Components | PUTATIVE PEPTIDASE C60B, SORTASE B | ||||||
Keywords | HYDROLASE / SORTASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | CLOSTRIDIUM DIFFICILE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Chambers, C.J. / Roberts, A.K. / Shone, C.C. / Acharya, K.R. | ||||||
Citation | Journal: Sci.Rep. / Year: 2015 Title: Structure and Function of a Clostridium Difficile Sortase Enzyme. Authors: Chambers, C.J. / Roberts, A.K. / Shone, C.C. / Acharya, K.R. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ux7.cif.gz | 97.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ux7.ent.gz | 75.6 KB | Display | PDB format |
PDBx/mmJSON format | 4ux7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ux7_validation.pdf.gz | 464.2 KB | Display | wwPDB validaton report |
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Full document | 4ux7_full_validation.pdf.gz | 466.8 KB | Display | |
Data in XML | 4ux7_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | 4ux7_validation.cif.gz | 22.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ux/4ux7 ftp://data.pdbj.org/pub/pdb/validation_reports/ux/4ux7 | HTTPS FTP |
-Related structure data
Related structure data | 1rz2S 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: 28320.658 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM DIFFICILE (bacteria) / Strain: 630 / Description: SYNTHETIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q183F3, sortase B #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | N-TERMINAL POLYHISTID | |
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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: 2.06 Å3/Da / Density % sol: 40.23 % / Description: NONE |
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Crystal grow | pH: 4.2 / Details: 0.1M PHOSPHATE-CITRATE PH 4.2, 40% PEG 300 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 4, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→29.37 Å / Num. obs: 15902 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 7.7 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.55→2.69 Å / Redundancy: 8 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 4.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: SWISS-MODELLER MODEL BASED ON PDB ENTRY 1RZ2 Resolution: 2.55→75 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.869 / SU B: 10.674 / SU ML: 0.231 / Cross valid method: THROUGHOUT / ESU R: 0.922 / ESU R Free: 0.328 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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 mean: 29.962 Å2
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Refinement step | Cycle: LAST / Resolution: 2.55→75 Å
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Refine LS restraints |
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