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- PDB-7esv: Structure and mutation analysis of the hexameric P4 from Pseudomo... -

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Basic information

Entry
Database: PDB / ID: 7esv
TitleStructure and mutation analysis of the hexameric P4 from Pseudomonas aeruginosa phage phiYY
ComponentsPackaging NTPase
KeywordsHYDROLASE / Cystoviruses / phiYY P4(aa1-291) / NTPase / VIRAL PROTEIN
Function / homologyPackaging enzyme P4 / ATPase P4 of dsRNA bacteriophage phi-12 / viral genome packaging / P-loop containing nucleoside triphosphate hydrolase / metal ion binding / D(-)-TARTARIC ACID / Packaging NTPase
Function and homology information
Biological speciesPseudomonas phage phiYY (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsZhang, C.Y. / Jin, T.C.
CitationJournal: Int.J.Biol.Macromol. / Year: 2022
Title: Structure and mutation analysis of the hexameric P4 from Pseudomonas aeruginosa phage phiYY.
Authors: Zhang, C. / Li, Y. / Samad, A. / Zheng, P. / Ji, Z. / Chen, F. / Zhang, H. / Jin, T.
History
DepositionMay 11, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

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Assembly

Deposited unit
B: Packaging NTPase
A: Packaging NTPase
C: Packaging NTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8484
Polymers92,6983
Non-polymers1501
Water1,18966
1
B: Packaging NTPase
A: Packaging NTPase
C: Packaging NTPase
hetero molecules

B: Packaging NTPase
A: Packaging NTPase
C: Packaging NTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,6978
Polymers185,3966
Non-polymers3002
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area19570 Å2
ΔGint-111 kcal/mol
Surface area56940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.630, 67.930, 107.650
Angle α, β, γ (deg.)90.000, 128.940, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Packaging NTPase


Mass: 30899.404 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage phiYY (virus) / Gene: phiYY_sL4 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1U9AK63
#2: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.39 Å3/Da / Density % sol: 48.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 200 mM NH4 tartrate, 20% PEG2000 MME, phosphate pH 7.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.18→33.57 Å / Num. obs: 304717 / % possible obs: 99.3 % / Redundancy: 6.7 % / CC1/2: 0.993 / Net I/σ(I): 8
Reflection shellResolution: 2.18→2.24 Å / Num. unique obs: 22749 / CC1/2: 0.64

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4blp

4blp


Resolution: 2.18→33.57 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 34.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2547 1988 4.37 %
Rwork0.2116 43494 -
obs0.2135 45482 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.03 Å2 / Biso mean: 51.5898 Å2 / Biso min: 31.58 Å2
Refinement stepCycle: final / Resolution: 2.18→33.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5835 0 10 66 5911
Biso mean--67.23 43.9 -
Num. residues----789
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.18-2.230.42851340.35683090322499
2.23-2.290.4161310.33643070320199
2.29-2.360.39681500.31783079322999
2.36-2.440.3211360.29943082321899
2.44-2.530.35841430.29053088323199
2.53-2.630.32351420.25883093323599
2.63-2.750.30071370.24613100323799
2.75-2.890.30931580.239530823240100
2.89-3.070.28381300.23463119324999
3.07-3.310.2771480.234831003248100
3.31-3.640.27321430.216531323275100
3.64-4.170.23821450.18633107325299
4.17-5.250.17521440.15933164330899
5.25-33.570.18671470.15683188333599

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