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- PDB-6kyd: Structure of the R217A mutant of Clostridium difficile sortase B -

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Basic information

Entry
Database: PDB / ID: 6kyd
TitleStructure of the R217A mutant of Clostridium difficile sortase B
ComponentsPutative peptidase C60B, sortase B
KeywordsHYDROLASE / sortase B / cysteine transpeptidase / Clostridium difficile
Function / homology
Function and homology information


hydrolase activity / membrane
Similarity search - Function
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 speciesClostridioides difficile 630 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsKang, 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
OrganizationGrant numberCountry
Ministry of Science and Technology (Taiwan)108-2320-B-006-012- Taiwan
CitationJournal: 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
DepositionSep 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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)26,1031
Polymers26,1031
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: fluorescence resonance energy transfer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9670 Å2
Unit cell
Length a, b, c (Å)120.895, 120.895, 120.895
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Putative peptidase C60B, sortase B


Mass: 26103.168 Da / Num. of mol.: 1 / Mutation: R217A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides 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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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.39 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 3.8 / Details: PEG3350, 0.1M glycine, 0.1M citric acid / PH range: 3.5-3.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.099→30 Å / Num. obs: 5156 / % possible obs: 94.1 % / Redundancy: 6.9 % / Biso Wilson estimate: 75.76 Å2 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.027 / Rrim(I) all: 0.073 / Χ2: 1.287 / Net I/σ(I): 16.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.1-3.217.30.3535260.9230.1390.380.872100
3.21-3.347.30.2565520.9650.1010.2760.979100
3.34-3.497.30.265400.9660.1020.281.296100
3.49-3.676.60.2424100.9640.1020.2641.34377.4
3.67-3.95.20.2234330.9690.110.2511.88578
3.9-4.216.90.0674660.9970.0270.0721.21186.9
4.21-4.637.10.0475510.9980.0180.0511.307100
4.63-5.2970.0585480.9970.0230.0631.425100
5.29-6.666.80.0555550.9980.0210.0591.74299.8
6.66-306.60.01857510.0070.021.09998.1

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GYJ

5gyj


Resolution: 3.1→28.495 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.31
RfactorNum. reflection% reflection
Rfree0.2553 356 6.98 %
Rwork0.2217 --
obs0.2242 5100 93.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 108.09 Å2 / Biso mean: 71.9127 Å2 / Biso min: 56.73 Å2
Refinement stepCycle: final / Resolution: 3.1→28.495 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1523 0 0 0 1523
Num. residues----183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071551
X-RAY DIFFRACTIONf_angle_d0.8592079
X-RAY DIFFRACTIONf_chiral_restr0.054225
X-RAY DIFFRACTIONf_plane_restr0.005260
X-RAY DIFFRACTIONf_dihedral_angle_d2.561944
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1-3.54650.32081110.27481675100
3.5465-4.46550.2978890.2402137380
4.4655-28.4950.22261560.1941169699
Refinement TLS params.Method: refined / Origin x: -8.7581 Å / Origin y: -34.7144 Å / Origin z: -41.9961 Å
111213212223313233
T0.5048 Å2-0.039 Å20.0765 Å2-0.5824 Å20.0701 Å2--0.3753 Å2
L2.0064 °2-0.5183 °20.3845 °2-4.9831 °20.5567 °2--1.151 °2
S0.0849 Å °-0.12 Å °0.0122 Å °0.3656 Å °0.0327 Å °0.2778 Å °-0.0446 Å °-0.2381 Å °-0.1588 Å °
Refinement TLS groupSelection details: all

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