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- PDB-4zrz: PlyCB mutant R66E -

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Basic information

Entry
Database: PDB / ID: 4zrz
TitlePlyCB mutant R66E
ComponentsPlyCB
KeywordsAntimicrobial protein / Viral protein / bacteriocidal / bacteriophage lysin / cell-binding subunit / octameric / cell-wall-cutting
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 / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsGallagher, D.T. / Nelson, D.C. / Shen, Y.
CitationJournal: Elife / Year: 2016
Title: A bacteriophage endolysin that eliminates intracellular streptococci.
Authors: Shen, Y. / Barros, M. / Vennemann, T. / Gallagher, D.T. / Yin, Y. / Linden, S.B. / Heselpoth, R.D. / Spencer, D.J. / Donovan, D.M. / Moult, J. / Fischetti, V.A. / Heinrich, F. / Losche, M. / Nelson, D.C.
History
DepositionMay 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Data collection / Source and taxonomy
Revision 1.2Jan 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Sep 27, 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: PlyCB
B: PlyCB


Theoretical massNumber of molelcules
Total (without water)15,6802
Polymers15,6802
Non-polymers00
Water1,892105
1
A: PlyCB
B: PlyCB

A: PlyCB
B: PlyCB

A: PlyCB
B: PlyCB

A: PlyCB
B: PlyCB


Theoretical massNumber of molelcules
Total (without water)62,7198
Polymers62,7198
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
Buried area12520 Å2
ΔGint-92 kcal/mol
Surface area22480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.428, 130.428, 130.428
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number211
Space group name H-MI432
Components on special symmetry positions
IDModelComponents
11B-131-

HOH

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Components

#1: Protein PlyCB


Mass: 7839.863 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus phage C1 (virus) / Gene: orf9 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7Y3F3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.95 Å3/Da / Density % sol: 58.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 14 mg/mL ptn, 43% MPD, 30 mM AmSO4, 70 mM Na Hepes

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.72→19.66 Å / Num. obs: 20025 / % possible obs: 98.1 % / Redundancy: 5.18 % / Rmerge(I) obs: 0.028 / Χ2: 0.98 / Net I/σ(I): 25.4 / Num. measured all: 104605 / Scaling rejects: 785
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
1.72-1.782.250.4172.7388117111.452485.2
1.78-1.853.190.2914.3617019121.397095.6
1.85-1.945.010.21861009219961.249299.8
1.94-2.045.760.1518.61176120201.1132100
2.04-2.175.810.10511.61182020170.96101100
2.17-2.335.850.077161193120190.8911299.9
2.33-2.575.880.06119.71202620320.8678100
2.57-2.945.920.042291216020450.8450100
2.94-3.75.890.02646.81225320730.8444100
3.7-19.665.650.01976.81251122000.9182100

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Processing

Software
NameVersionClassification
d*TREK9.9.8.6 W9RSSIdata reduction
d*TREK9.9.8.6 W9RSSIdata scaling
REFMAC5.8.0103refinement
PDB_EXTRACT3.15data extraction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F87

4f87


Resolution: 1.72→14 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.2492 / WRfactor Rwork: 0.2174 / FOM work R set: 0.8182 / SU B: 2.181 / SU ML: 0.071 / SU R Cruickshank DPI: 0.1022 / SU Rfree: 0.1034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2492 1030 5.2 %RANDOM
Rwork0.2174 ---
obs0.219 18961 97.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.67 Å2 / Biso mean: 33.254 Å2 / Biso min: 19 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.72→14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms944 0 0 105 1049
Biso mean---47.98 -
Num. residues----124
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.019958
X-RAY DIFFRACTIONr_bond_other_d0.0020.02900
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.9341289
X-RAY DIFFRACTIONr_angle_other_deg0.94232069
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6515122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.0782645
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.47215163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.521152
X-RAY DIFFRACTIONr_chiral_restr0.0950.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021108
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02218
X-RAY DIFFRACTIONr_mcbond_it2.3183.134494
X-RAY DIFFRACTIONr_mcbond_other2.3123.125493
X-RAY DIFFRACTIONr_mcangle_it3.5654.659614
LS refinement shellResolution: 1.72→1.764 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.443 49 -
Rwork0.4 1181 -
all-1230 -
obs--83.28 %

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