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- PDB-4f88: X-ray Crystal Structure of PlyC -

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Basic information

Entry
Database: PDB / ID: 4f88
TitleX-ray Crystal Structure of PlyC
Components
  • PlyCA
  • PlyCB
KeywordsAntimicrobial protein / viral protein / Lysin / bacteriophage
Function / homology
Function and homology information


killing of cells of another organism / identical protein binding
Similarity search - Function
endopeptidase fold (from Nostoc punctiforme) - #60 / Signal recognition particle alu RNA binding heterodimer, srp9/1 - #190 / : / Streptococcus virus C1, PlyCB / CHAP domain profile. / CHAP domain / CHAP domain / Signal recognition particle alu RNA binding heterodimer, srp9/1 / endopeptidase fold (from Nostoc punctiforme) / Alpha-Beta Complex ...endopeptidase fold (from Nostoc punctiforme) - #60 / Signal recognition particle alu RNA binding heterodimer, srp9/1 - #190 / : / Streptococcus virus C1, PlyCB / CHAP domain profile. / CHAP domain / CHAP domain / Signal recognition particle alu RNA binding heterodimer, srp9/1 / endopeptidase fold (from Nostoc punctiforme) / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PlyCA / Endolysin PlyC, small cell-wall binding subunit
Similarity search - Component
Biological speciesStreptococcus phage C1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsMcGowan, S. / Buckle, A.M. / Fischetti, V.A. / Nelson, D.C. / Whisstock, J.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: X-ray crystal structure of the streptococcal specific phage lysin PlyC.
Authors: McGowan, S. / Buckle, A.M. / Mitchell, M.S. / Hoopes, J.T. / Gallagher, D.T. / Heselpoth, R.D. / Shen, Y. / Reboul, C.F. / Law, R.H. / Fischetti, V.A. / Whisstock, J.C. / Nelson, D.C.
History
DepositionMay 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2012Group: Database references
Revision 1.2Aug 15, 2012Group: Database references
Revision 1.3Sep 13, 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

Downloads & links

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Assembly

Deposited unit
1: PlyCA
2: PlyCA
A: PlyCB
B: PlyCB
C: PlyCB
D: PlyCB
E: PlyCB
F: PlyCB
G: PlyCB
H: PlyCB
I: PlyCB
J: PlyCB
K: PlyCB
L: PlyCB
M: PlyCB
N: PlyCB
O: PlyCB
P: PlyCB


Theoretical massNumber of molelcules
Total (without water)229,04018
Polymers229,04018
Non-polymers00
Water0
1
1: PlyCA
A: PlyCB
B: PlyCB
C: PlyCB
D: PlyCB
E: PlyCB
F: PlyCB
G: PlyCB
H: PlyCB


Theoretical massNumber of molelcules
Total (without water)114,5209
Polymers114,5209
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17770 Å2
ΔGint-124 kcal/mol
Surface area41750 Å2
MethodPISA
2
2: PlyCA
I: PlyCB
J: PlyCB
K: PlyCB
L: PlyCB
M: PlyCB
N: PlyCB
O: PlyCB
P: PlyCB


Theoretical massNumber of molelcules
Total (without water)114,5209
Polymers114,5209
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.853, 117.423, 222.192
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PlyCA


Mass: 50526.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus phage C1 (virus) / Gene: orf11 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Y3F1
#2: Protein
PlyCB


Mass: 7999.139 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus phage C1 (virus) / Gene: orf9 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Y3F3

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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: 2.67 Å3/Da / Density % sol: 53.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.1 M Hepes, 12% PEG4000, 10% isopropanol, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1.4 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 3, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4 Å / Relative weight: 1
ReflectionResolution: 3.2→103.7 Å / Num. obs: 40690 / % possible obs: 99.2 % / Redundancy: 4 % / Biso Wilson estimate: 107.71 Å2 / Rmerge(I) obs: 0.1
Reflection shellResolution: 3.2→3.48 Å / Rmerge(I) obs: 0.658 / % possible all: 96.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
BUSTER2.8.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4F87

4f87


Resolution: 3.3→46.72 Å / Cor.coef. Fo:Fc: 0.8748 / Cor.coef. Fo:Fc free: 0.839 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.297 1868 5 %RANDOM
Rwork0.2655 ---
obs0.267 37352 99.03 %-
Displacement parametersBiso mean: 98.45 Å2
Baniso -1Baniso -2Baniso -3
1--8.4574 Å20 Å20 Å2
2--7.6384 Å20 Å2
3---0.819 Å2
Refine analyzeLuzzati coordinate error obs: 0.837 Å
Refinement stepCycle: LAST / Resolution: 3.3→46.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12281 0 0 0 12281
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00812484HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.117041HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3590SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes251HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1978HARMONIC5
X-RAY DIFFRACTIONt_it12484HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.63
X-RAY DIFFRACTIONt_other_torsion20.95
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1825SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact13104SEMIHARMONIC4
LS refinement shellResolution: 3.3→3.39 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2841 128 4.64 %
Rwork0.2495 2632 -
all0.2511 2760 -
obs--99.03 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.3639-0.06370.40961.249-0.06311.8805-0.0077-0.20330.03860.23110.1641-0.0543-0.31910.0009-0.1564-0.12890.1929-0.0426-0.2809-0.05350.0093-21.3041-14.9034-30.1116
20.0097-0.6309-0.19482.41080.7743.8657-0.0010.1953-0.0025-0.08860.0345-0.00380.00720.0064-0.03350.0196-0.09850.05650.0171-0.0788-0.084-15.253-13.01948.9474
31.5926-0.03340.47122.73822.58821.22350.00860.1817-0.0878-0.1491-0.0394-0.026-0.0475-0.05140.0308-0.0083-0.1594-0.03240-0.0236-0.0367-31.2499-9.125415.2062
40.8775-0.5782-0.97982.2180.53820.6211-0.01090.0161-0.0849-0.02980.010.0429-0.1047-0.20460.00090.0463-0.11270.0016-0.0640.0224-0.1219-39.1791-5.104630.6829
52.20491.2956-0.54730.9138-0.29880.749-0.0184-0.01010.0097-0.01480.0347-0.0440.0627-0.1352-0.01620.0336-0.0078-0.05520.0094-0.0175-0.1419-35.8943-3.837148.6384
62.39290.27640.43961.89620.15920.6219-0.0129-0.11140.0003-0.00660.015-0.05980.0031-0.08-0.002-0.07530.13840.0307-0.04120.0194-0.0332-18.6219-5.964457.6492
72.7036-2.9961-0.04224.6235-0.42432.4659-0.0084-0.03640.006-0.02370.01790.03860.00980.0057-0.0095-0.06570.1152-0.0047-0.217-0.01270.0242-1.3499-11.793751.5715
81.49871.33221.75062.31070.0682.0124-0.00010.05310.0109-0.04640.0488-0.01610.05790.0956-0.04870.05160.09570.1139-0.1611-0.04510.00685.9308-15.059433.9658
90.9905-2.1746-1.74911.14371.22032.5670.00220.15110.06050.0275-0.0289-0.00280.10050.14960.02670.1646-0.04390.03760.0374-0.1083-0.19090.2439-15.43216.9811
101.50791.09520.76331.83742.18921.882-0.0061-0.0644-0.01060.05290.0079-0.00410.020.0067-0.00180.106-0.1186-0.07560.058-0.12640.1116.092211.55112.4
110.00030.2864-1.65073.59160.90151.4055-0.0066-0.08660.04160.05310.0154-0.0312-0.05170.0022-0.00880.1775-0.0856-0.04480.0508-0.10950.03380.481622.991-6.3386
1200.03380.05111.4012-0.0032.1952-0.00120.0030.04220.0279-0.0215-0.0055-0.0064-0.00450.02270.0791-0.0461-0.0532-0.0672-0.07090.0952-1.466331.2623-21.0581
130.16390.8686-0.51340.3124-0.70650.1919-0.00620.02360.02660.01080.00440.0353-0.02160.00430.00190.0604-0.1216-0.0714-0.0709-0.08810.0695-1.500427.4637-38.2577
141.01750.0477-0.05511.68170.99160.36230.00480.04910.0844-0.02050.00140.008-0.0978-0.0448-0.0061-0.1362-0.1634-0.0272-0.04060.0895-0.00972.739810.8032-45.9213
151.72120.3947-0.04690.6963-1.09950.61220.0036-0.03740.0079-0.0306-0.0021-0.02820.06860.0597-0.0015-0.18820.0101-0.02720.0111-0.06170.021710.196-6.0307-39.919
162.0619-0.7733-0.8270.4584-0.02820.48740.0118-0.01130.04110.0601-0.0422-0.00290.03540.07240.03040.01570.0035-0.09610.15240.0808-0.112813.8275-12.0431-21.0909
171.71120.6042.79111.05790.25551.3979-0.0068-0.06830.0190.0623-0.03260.02080.03140.04610.03950.0889-0.1-0.0830.195-0.0163-0.047613.3285-4.9856-3.9896
181.06950.28990.47671.48750.46882.8802-0.08970.19580.0606-0.16210.1258-0.16010.16220.4518-0.0361-0.2227-0.03880.0133-0.2623-0.08570.1458-0.865221.458242.5078
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION122 - 462
2X-RAY DIFFRACTION2A3 - 70
3X-RAY DIFFRACTION3B1 - 70
4X-RAY DIFFRACTION4C2 - 70
5X-RAY DIFFRACTION5D8 - 70
6X-RAY DIFFRACTION6E6 - 70
7X-RAY DIFFRACTION7F6 - 70
8X-RAY DIFFRACTION8G2 - 70
9X-RAY DIFFRACTION9H3 - 70
10X-RAY DIFFRACTION10I3 - 67
11X-RAY DIFFRACTION11J2 - 68
12X-RAY DIFFRACTION12K3 - 69
13X-RAY DIFFRACTION13L9 - 70
14X-RAY DIFFRACTION14M6 - 70
15X-RAY DIFFRACTION15N11 - 70
16X-RAY DIFFRACTION16O5 - 70
17X-RAY DIFFRACTION17P8 - 70
18X-RAY DIFFRACTION1812 - 464

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