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- PDB-5yfk: X-ray structure of a mutant form C232S of Clostridium perfringens... -

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Basic information

Entry
Database: PDB / ID: 5yfk
TitleX-ray structure of a mutant form C232S of Clostridium perfringens sortase B
ComponentsUncharacterized protein Sortase B
KeywordsTRANSFERASE / cystein transpeptidase / sortase
Function / homology
Function and homology information


Sortase B, Firmicutes / Sortase B family / Sortase; Chain: A; / Sortase / Sortase family / Sortase domain superfamily / Sortase domain / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKamitori, S. / Tamai, E.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSPS KAKENHIJP15K06973, JP15K08482 Japan
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: X-ray structure of Clostridium perfringens sortase B cysteine transpeptidase
Authors: Tamai, E. / Sekiya, H. / Maki, J. / Nariya, H. / Yoshida, H. / Kamitori, S.
History
DepositionSep 21, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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: Uncharacterized protein Sortase B


Theoretical massNumber of molelcules
Total (without water)27,7751
Polymers27,7751
Non-polymers00
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.670, 59.730, 56.220
Angle α, β, γ (deg.)90.00, 121.39, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-339-

HOH

21A-386-

HOH

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Components

#1: Protein Uncharacterized protein Sortase B


Mass: 27774.691 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 24-249 / Mutation: C232S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (strain 13 / Type A) (bacteria)
Strain: 13 / Type A / Gene: CPE0513 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8XN25
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 1.93 Å3/Da / Density % sol: 36.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 200mM ammonium phosphate monobasic, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→47.99 Å / Num. obs: 19621 / % possible obs: 99.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 20.6
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 5384 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B23

5b23


Resolution: 1.8→47.99 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.131 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.133 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22788 1002 5.1 %RANDOM
Rwork0.18197 ---
obs0.18439 18619 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.287 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.8→47.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1757 0 0 133 1890
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191793
X-RAY DIFFRACTIONr_angle_refined_deg1.021.9352412
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 82 -
Rwork0.27 1373 -
obs--99.86 %

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