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- PDB-5gyj: Structure of catalytically active sortase from Clostridium difficile -

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Basic information

Entry
Database: PDB / ID: 5gyj
TitleStructure of catalytically active sortase from Clostridium difficile
ComponentsPutative peptidase C60B, sortase B
KeywordsHYDROLASE / transpeptidase / Cys-His-Arg catalytic triad
Function / homology
Function and homology information


Sortase B family / Sortase; Chain: A; / Sortase / Sortase family / Sortase domain superfamily / Sortase domain / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Peptidase C60B, sortase B
Similarity search - Component
Biological speciesPeptoclostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.801 Å
AuthorsYin, J.-C. / Fei, C.-H. / Hsiao, Y.-Y. / Nix, J.C. / Huang, I.-H. / Wang, S.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and TechnologyMOST 104-2320-B-006-050 Taiwan
CitationJournal: Front Cell Infect Microbiol / Year: 2016
Title: Structural Insights into Substrate Recognition by Clostridium difficile Sortase.
Authors: Yin, J.C. / Fei, C.H. / Lo, Y.C. / Hsiao, Y.Y. / Chang, J.C. / Nix, J.C. / Chang, Y.Y. / Yang, L.W. / Huang, I.H. / Wang, S.
History
DepositionSep 22, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 4, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative peptidase C60B, sortase B


Theoretical massNumber of molelcules
Total (without water)26,1891
Polymers26,1891
Non-polymers00
Water68538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.250, 121.250, 121.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Putative peptidase C60B, sortase B


Mass: 26189.283 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 28-224
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Peptoclostridium difficile (strain 630) (bacteria)
Strain: 630 / Gene: CD630_27180 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q183F3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.29 % / Description: cubic 0.3 micrometer in diameter
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 0.1M citric acid, pH3.5, 0.1M glycine, 24% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→25.9 Å / Num. obs: 7031 / % possible obs: 94.1 % / Redundancy: 9.3 % / Biso Wilson estimate: 55.74 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 45.85
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.259 / Mean I/σ(I) obs: 10.4 / % possible all: 100

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QWZ

1qwz


Resolution: 2.801→25.851 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.73
RfactorNum. reflection% reflectionSelection details
Rfree0.2523 352 5.04 %Random
Rwork0.1971 ---
obs0.1999 6990 93.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 50.1514 Å2
Refinement stepCycle: LAST / Resolution: 2.801→25.851 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1529 0 0 38 1567
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011557
X-RAY DIFFRACTIONf_angle_d1.2052086
X-RAY DIFFRACTIONf_dihedral_angle_d15.374591
X-RAY DIFFRACTIONf_chiral_restr0.042225
X-RAY DIFFRACTIONf_plane_restr0.004261
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8009-3.20550.31931230.23852330X-RAY DIFFRACTION100
3.2055-4.03620.26911030.22011942X-RAY DIFFRACTION83
4.0362-25.85170.2221260.17262366X-RAY DIFFRACTION98

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