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

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Basic information

Entry
Database: PDB / ID: 7esp
TitleStructure and mutation analysis of the hexameric P4 from Pseudomonas aeruginosa phage phiYY
ComponentsPackaging NTPase
KeywordsHYDROLASE / Cystoviruses / phiYY P4 / 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 / DI(HYDROXYETHYL)ETHER / D(-)-TARTARIC ACID / Packaging NTPase
Function and homology information
Biological speciesPseudomonas phage phiYY (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 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

Downloads & links

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Assembly

Deposited unit
A: Packaging NTPase
B: Packaging NTPase
C: Packaging NTPase
D: Packaging NTPase
E: Packaging NTPase
F: Packaging NTPase
G: Packaging NTPase
H: Packaging NTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)300,33320
Polymers298,7088
Non-polymers1,62512
Water6,107339
1
A: Packaging NTPase
B: Packaging NTPase
C: Packaging NTPase
D: Packaging NTPase
E: Packaging NTPase
F: Packaging NTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,25015
Polymers224,0316
Non-polymers1,2199
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20670 Å2
ΔGint-105 kcal/mol
Surface area58200 Å2
MethodPISA
2
G: Packaging NTPase
H: Packaging NTPase
hetero molecules

G: Packaging NTPase
H: Packaging NTPase
hetero molecules

G: Packaging NTPase
H: Packaging NTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,25015
Polymers224,0316
Non-polymers1,2199
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area20610 Å2
ΔGint-101 kcal/mol
Surface area57710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)240.126, 240.126, 152.401
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
Packaging NTPase


Mass: 37338.531 Da / Num. of mol.: 8
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.: 8 / Source method: obtained synthetically / Formula: C4H6O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.83 Å3/Da / Density % sol: 56.55 %
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: Nov 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.43→40.97 Å / Num. obs: 1250846 / % possible obs: 97.8 % / Redundancy: 10.3 % / CC1/2: 0.998 / Net I/σ(I): 15.7
Reflection shellResolution: 2.43→2.56 Å / Num. unique obs: 198187 / CC1/2: 0.834

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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: 2.43→40.97 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 24.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2167 2004 1.65 %
Rwork0.1781 119252 -
obs0.1787 121256 97.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.52 Å2 / Biso mean: 61.5639 Å2 / Biso min: 34.79 Å2
Refinement stepCycle: final / Resolution: 2.43→40.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15500 0 108 339 15947
Biso mean--82.92 54.69 -
Num. residues----2091
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.43-2.490.3211460.25458683100
2.49-2.550.29381410.23338718100
2.55-2.630.25021540.2398706100
2.63-2.710.28541300.2278738685
2.71-2.810.27191510.23238699100
2.81-2.920.29341360.2238697100
2.92-3.060.24481500.21978720100
3.06-3.220.2471380.20468719100
3.22-3.420.23061550.20618697100
3.42-3.680.22081130.1811745886
3.68-4.050.20041480.17318684100
4.05-4.640.17771470.14158725100
4.64-5.840.19631410.16188678100
5.84-40.970.1841540.14268682100

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