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

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Basic information

Entry
Database: PDB / ID: 7eso
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 / Packaging NTPase
Function and homology information
Biological speciesPseudomonas phage phiYY (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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
H: Packaging NTPase
G: Packaging NTPase
C: Packaging NTPase
D: Packaging NTPase
E: Packaging NTPase
F: Packaging NTPase


Theoretical massNumber of molelcules
Total (without water)301,5758
Polymers301,5758
Non-polymers00
Water4,414245
1
A: Packaging NTPase
B: Packaging NTPase
C: Packaging NTPase
D: Packaging NTPase
E: Packaging NTPase
F: Packaging NTPase


Theoretical massNumber of molelcules
Total (without water)226,1816
Polymers226,1816
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17750 Å2
ΔGint-114 kcal/mol
Surface area57930 Å2
MethodPISA
2
H: Packaging NTPase
G: Packaging NTPase

H: Packaging NTPase
G: Packaging NTPase

H: Packaging NTPase
G: Packaging NTPase


Theoretical massNumber of molelcules
Total (without water)226,1816
Polymers226,1816
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area17540 Å2
ΔGint-114 kcal/mol
Surface area58030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)241.075, 241.075, 152.950
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: 37696.875 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.72 Å3/Da / Density % sol: 57.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 600 mM K/Na tartrate, 100 mM Tris-HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
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: 2.4→41.13 Å / Num. obs: 242159 / % possible obs: 99.7 % / Redundancy: 10.2 % / CC1/2: 0.995 / Rrim(I) all: 0.167 / Net I/σ(I): 10.3
Reflection shellResolution: 2.4→2.44 Å / Mean I/σ(I) obs: 2.4 / Num. unique obs: 62177 / CC1/2: 0.694 / Rrim(I) all: 0.12
Serial crystallography sample deliveryMethod: injection

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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: 2.45→41.13 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 22.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2076 12121 5.01 %
Rwork0.1803 229745 -
obs0.1817 241866 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.95 Å2 / Biso mean: 58.4117 Å2 / Biso min: 28.68 Å2
Refinement stepCycle: final / Resolution: 2.45→41.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15452 0 0 245 15697
Biso mean---50.36 -
Num. residues----2092
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.45-2.480.33654580.28677928250100
2.48-2.510.30393540.257277208074100
2.51-2.540.27774000.246676058005100
2.54-2.570.27424120.239677638175100
2.57-2.610.27934160.241475347950100
2.61-2.640.25664280.236278228250100
2.64-2.680.29443660.244875597925100
2.68-2.720.25664270.222776188045100
2.72-2.760.26743790.232376708049100
2.76-2.810.23834260.223676468072100
2.81-2.860.26874190.214476408059100
2.86-2.910.283680.216577438111100
2.91-2.960.24174280.206976428070100
2.96-3.030.24283900.202877208110100
3.03-3.090.26784060.206177128118100
3.09-3.160.23094060.21175787984100
3.16-3.240.24693610.207477218082100
3.24-3.330.23864030.211376938096100
3.33-3.430.2353990.20776098008100
3.43-3.540.25094270.203577618188100
3.54-3.660.23523600.19357602796299
3.66-3.810.19624260.18197627805399
3.81-3.980.18744090.17757555796499
3.98-4.190.17273970.14987585798299
4.19-4.460.1713840.14267587797199
4.46-4.80.16534070.131277128119100
4.8-5.280.15524260.148976748100100
5.28-6.040.20994180.15875858003100
6.05-7.610.19094110.157976428053100
7.61-41.130.12874100.13817628803899
Refinement TLS params.Method: refined / Origin x: -49.6075 Å / Origin y: -30.9441 Å / Origin z: -57.5306 Å
111213212223313233
T0.3482 Å20.0162 Å2-0.0393 Å2-0.3561 Å2-0.0066 Å2--0.3674 Å2
L0.3003 °20.0413 °2-0.1542 °2-0.2279 °2-0.0061 °2--0.3356 °2
S-0.0691 Å °0.0747 Å °0.0564 Å °0.0658 Å °0.056 Å °0.0301 Å °0.0578 Å °-0.1071 Å °0.0134 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA28 - 296
2X-RAY DIFFRACTION1allB28 - 288
3X-RAY DIFFRACTION1allH28 - 296
4X-RAY DIFFRACTION1allG28 - 288
5X-RAY DIFFRACTION1allC28 - 296
6X-RAY DIFFRACTION1allD28 - 288
7X-RAY DIFFRACTION1allE28 - 296
8X-RAY DIFFRACTION1allF28 - 288
9X-RAY DIFFRACTION1allI1 - 245

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