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- PDB-6kyc: Structure of the S207A mutant of Clostridium difficile sortase B -

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Basic information

Entry
Database: PDB / ID: 6kyc
TitleStructure of the S207A 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 speciesPeptoclostridium difficile 630 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.604 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)107-2320-B-006-048- 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 17, 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)26,1731
Polymers26,1731
Non-polymers00
Water43224
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 area9780 Å2
Unit cell
Length a, b, c (Å)120.969, 120.969, 120.969
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: 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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.82 Å3/Da / Density % sol: 56.35 %
Crystal growTemperature: 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

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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: Oct 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.695.30.7158780.7320.3310.7930.85498.7
2.69-2.87.10.468980.8860.1840.4970.79100
2.8-2.937.40.2869130.9570.1120.3080.823100
2.93-3.087.40.1749330.9810.0680.1880.844100
3.08-3.287.40.1038960.9920.040.1110.932100
3.28-3.537.40.0728980.9950.0280.0771.041100
3.53-3.887.30.0529370.9980.020.0561.065100
3.88-4.447.20.0399070.9990.0150.0420.95199.8
4.44-5.597.10.0429330.9980.0170.0461.32699.1
5.59-306.90.0269340.9990.010.0280.70696.5

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Processing

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

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
RfactorNum. reflection% reflection
Rfree0.2415 463 5.17 %
Rwork0.2151 8498 -
obs0.2165 8961 97.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.41 Å2 / Biso mean: 44.4123 Å2 / Biso min: 16.96 Å2
Refinement stepCycle: final / Resolution: 2.604→28.513 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1528 0 0 24 1552
Biso mean---38.22 -
Num. residues----183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021556
X-RAY DIFFRACTIONf_angle_d0.4382085
X-RAY DIFFRACTIONf_chiral_restr0.042225
X-RAY DIFFRACTIONf_plane_restr0.002261
X-RAY DIFFRACTIONf_dihedral_angle_d2.106948
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.604-2.98050.33191640.2658268094
2.9805-3.75380.24511490.23592892100
3.7538-28.5130.2121500.1869292698
Refinement TLS params.Method: refined / Origin x: -8.9583 Å / Origin y: -34.8259 Å / Origin z: -42.0221 Å
111213212223313233
T0.2324 Å2-0.0351 Å20.0398 Å2-0.2583 Å20.0291 Å2--0.1157 Å2
L0.1783 °2-0.1706 °20.0459 °2-0.2727 °2-0.0134 °2--0.048 °2
S0.1077 Å °-0.2463 Å °-0.0701 Å °0.1972 Å °0.033 Å °0.2669 Å °-0.2434 Å °-0.0782 Å °0.0263 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA29 - 224
2X-RAY DIFFRACTION1allS1 - 47

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