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- PDB-4f87: X-ray Crystal Structure of PlyCB -

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Basic information

Entry
Database: PDB / ID: 4f87
TitleX-ray Crystal Structure of PlyCB
ComponentsPlyCB
KeywordsANTIMICROBIAL PROTEIN / VIRAL PROTEIN / Lysin / bacteriophage
Function / homologySignal recognition particle alu RNA binding heterodimer, srp9/1 - #190 / : / Streptococcus virus C1, PlyCB / Signal recognition particle alu RNA binding heterodimer, srp9/1 / killing of cells of another organism / 2-Layer Sandwich / identical protein binding / Alpha Beta / Endolysin PlyC, small cell-wall binding subunit
Function and homology information
Biological speciesStreptococcus phage C1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / S-SAD / Resolution: 1.4 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 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PlyCB
B: PlyCB
C: PlyCB
D: PlyCB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2336
Polymers31,9974
Non-polymers2362
Water6,720373
1
A: PlyCB
B: PlyCB
C: PlyCB
D: PlyCB
hetero molecules

A: PlyCB
B: PlyCB
C: PlyCB
D: PlyCB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,46612
Polymers63,9938
Non-polymers4734
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area13210 Å2
ΔGint-116 kcal/mol
Surface area22830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.968, 130.968, 130.968
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein
PlyCB


Mass: 7999.139 Da / Num. of mol.: 4
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
#2: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 373 / 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: 2.93 Å3/Da / Density % sol: 57.95 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6
Details: 25% MPD, 0.1 M Hepes, 0.2 M Sodium citrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONAPS 17-BM11.4
ROTATING ANODERIGAKU21.5418
Detector
TypeIDDetectorDate
ADSC QUANTUM 210r1CCDApr 3, 2006
RIGAKU RAXIS IV2IMAGE PLATEFeb 17, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Osmic MirrorsSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.41
21.54181
ReflectionResolution: 1.4→30 Å / Num. obs: 71861 / % possible obs: 98.4 % / Redundancy: 7.1 % / Biso Wilson estimate: 20.45 Å2 / Rmerge(I) obs: 0.056
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.58 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
autoSHARPphasing
BUSTER2.8.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: S-SAD / Resolution: 1.4→28 Å / Cor.coef. Fo:Fc: 0.9516 / Cor.coef. Fo:Fc free: 0.9533 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.1974 3682 5.13 %RANDOM
Rwork0.1868 ---
obs0.1873 71843 --
Displacement parametersBiso mean: 25.55 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.179 Å
Refinement stepCycle: LAST / Resolution: 1.4→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1864 0 16 373 2253
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011941HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.12623HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d680SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes48HARMONIC2
X-RAY DIFFRACTIONt_gen_planes295HARMONIC5
X-RAY DIFFRACTIONt_it1927HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion4.49
X-RAY DIFFRACTIONt_other_torsion14.12
X-RAY DIFFRACTIONt_chiral_improper_torsion271SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2669SEMIHARMONIC4
LS refinement shellResolution: 1.4→1.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2268 245 4.71 %
Rwork0.2023 4958 -
all0.2034 5203 -
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)
10.87041.2362-0.02332.27240.20740.4155-0.04580.06340.0487-0.06990.04790.0691-0.01680.0072-0.0021-0.04230.01210.0004-0.03570.00340.042322.7174-13.047145.5995
22.24-1.2727-0.25670.9739-0.00310.41690.04830.0735-0.078-0.0707-0.05080.0558-0.0096-0.01890.0026-0.0389-0.0128-0.0037-0.0435-0.00020.042512.940322.545.4249
30.466-0.4503-0.44522.84570.23280.342-0.04650.0261-0.054-0.14070.03380.1124-0.01120.00460.0127-0.0454-0.0029-0.0128-0.0266-0.01090.034624.90436.804145.398
42.93810.4536-0.24450.4343-0.46830.39020.03410.1465-0.1058-0.0308-0.0432-0.058-0.006-0.0140.009-0.02910.00270.0112-0.0474-0.01430.0323-6.906224.931145.368
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 70
2X-RAY DIFFRACTION2B9 - 70
3X-RAY DIFFRACTION3C9 - 70
4X-RAY DIFFRACTION4D9 - 70

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