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- PDB-7kwt: X-ray Crystal Structure of PlyCB Mutant Y28H -

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Basic information

Entry
Database: PDB / ID: 7kwt
TitleX-ray Crystal Structure of PlyCB Mutant Y28H
ComponentsPlyCB
KeywordsANTIMICROBIAL PROTEIN / ENDOLYSIN / VIRAL PROTEIN / PHAGE EFFECTOR PROTEIN
Function / homology: / Streptococcus virus C1, PlyCB / killing of cells of another organism / identical protein binding / Endolysin PlyC, small cell-wall binding subunit
Function and homology information
Biological speciesStreptococcus virus C1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsWilliams, D.E. / Broendum, S.S. / Hayes, B.K. / Drinkwater, N. / McGowan, S.
CitationJournal: Mol.Microbiol. / Year: 2021
Title: High avidity drives the interaction between the streptococcal C1 phage endolysin, PlyC, with the cell surface carbohydrates of Group A Streptococcus.
Authors: Broendum, S.S. / Williams, D.E. / Hayes, B.K. / Kraus, F. / Fodor, J. / Clifton, B.E. / Geert Volbeda, A. / Codee, J.D.C. / Riley, B.T. / Drinkwater, N. / Farrow, K.A. / Tsyganov, K. / ...Authors: Broendum, S.S. / Williams, D.E. / Hayes, B.K. / Kraus, F. / Fodor, J. / Clifton, B.E. / Geert Volbeda, A. / Codee, J.D.C. / Riley, B.T. / Drinkwater, N. / Farrow, K.A. / Tsyganov, K. / Heselpoth, R.D. / Nelson, D.C. / Jackson, C.J. / Buckle, A.M. / McGowan, S.
History
DepositionDec 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 8, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PlyCB
B: PlyCB


Theoretical massNumber of molelcules
Total (without water)15,6862
Polymers15,6862
Non-polymers00
Water2,522140
1
A: PlyCB
B: PlyCB

A: PlyCB
B: PlyCB

A: PlyCB
B: PlyCB

A: PlyCB
B: PlyCB


Theoretical massNumber of molelcules
Total (without water)62,7438
Polymers62,7438
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation15_565y,-x+1,z1
crystal symmetry operation16_655-y+1,x,z1
Buried area13360 Å2
ΔGint-93 kcal/mol
Surface area22920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.154, 131.154, 131.154
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number211
Space group name H-MI432
Space group name HallI423
Symmetry operation#1: x,y,z
#2: x,-z,y
#3: x,z,-y
#4: z,y,-x
#5: -z,y,x
#6: -y,x,z
#7: y,-x,z
#8: z,x,y
#9: y,z,x
#10: -y,-z,x
#11: z,-x,-y
#12: -y,z,-x
#13: -z,-x,y
#14: -z,x,-y
#15: y,-z,-x
#16: x,-y,-z
#17: -x,y,-z
#18: -x,-y,z
#19: y,x,-z
#20: -y,-x,-z
#21: z,-y,x
#22: -z,-y,-x
#23: -x,z,y
#24: -x,-z,-y
#25: x+1/2,y+1/2,z+1/2
#26: x+1/2,-z+1/2,y+1/2
#27: x+1/2,z+1/2,-y+1/2
#28: z+1/2,y+1/2,-x+1/2
#29: -z+1/2,y+1/2,x+1/2
#30: -y+1/2,x+1/2,z+1/2
#31: y+1/2,-x+1/2,z+1/2
#32: z+1/2,x+1/2,y+1/2
#33: y+1/2,z+1/2,x+1/2
#34: -y+1/2,-z+1/2,x+1/2
#35: z+1/2,-x+1/2,-y+1/2
#36: -y+1/2,z+1/2,-x+1/2
#37: -z+1/2,-x+1/2,y+1/2
#38: -z+1/2,x+1/2,-y+1/2
#39: y+1/2,-z+1/2,-x+1/2
#40: x+1/2,-y+1/2,-z+1/2
#41: -x+1/2,y+1/2,-z+1/2
#42: -x+1/2,-y+1/2,z+1/2
#43: y+1/2,x+1/2,-z+1/2
#44: -y+1/2,-x+1/2,-z+1/2
#45: z+1/2,-y+1/2,x+1/2
#46: -z+1/2,-y+1/2,-x+1/2
#47: -x+1/2,z+1/2,y+1/2
#48: -x+1/2,-z+1/2,-y+1/2
Components on special symmetry positions
IDModelComponents
11A-171-

HOH

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Components

#1: Protein PlyCB


Mass: 7842.917 Da / Num. of mol.: 2 / Mutation: Y28H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus virus C1 / Gene: orf9 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Y3F3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 3 Å3/Da / Density % sol: 58.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: 0.1M HEPES (pH 6.0), 0.2M sodium citrate, 25% methylpentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95366 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95366 Å / Relative weight: 1
ReflectionResolution: 1.79→41.47 Å / Num. obs: 18530 / % possible obs: 99.88 % / Redundancy: 2 % / Biso Wilson estimate: 32.74 Å2 / CC1/2: 1 / CC star: 1 / Net I/σ(I): 26.55
Reflection shellResolution: 1.79→1.851 Å / Num. unique obs: 1786 / CC1/2: 0.925 / CC star: 0.98

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F87

4f87


Resolution: 1.79→41.47 Å / SU ML: 0.1528 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.7969
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2055 908 4.9 %
Rwork0.1893 17617 -
obs0.1901 18525 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.56 Å2
Refinement stepCycle: LAST / Resolution: 1.79→41.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms967 0 0 140 1107
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033981
X-RAY DIFFRACTIONf_angle_d0.60671320
X-RAY DIFFRACTIONf_chiral_restr0.0526149
X-RAY DIFFRACTIONf_plane_restr0.0037174
X-RAY DIFFRACTIONf_dihedral_angle_d15.9392350
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.90.24451420.21572865X-RAY DIFFRACTION99.47
1.9-2.050.24451360.19592889X-RAY DIFFRACTION100
2.05-2.250.20861620.18442887X-RAY DIFFRACTION100
2.25-2.580.20921410.19272926X-RAY DIFFRACTION99.97
2.58-3.250.24361640.20022945X-RAY DIFFRACTION100
3.25-41.470.18251630.18173105X-RAY DIFFRACTION100

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