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- PDB-7chu: Geobacillus virus E2 - ORF18 -

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Basic information

Entry
Database: PDB / ID: 7chu
TitleGeobacillus virus E2 - ORF18
ComponentsPutative pectin lyase
KeywordsCELL INVASION / Tailspike protein / Thermophilic bacteriophage
Function / homology
Function and homology information


virus tail / lyase activity / symbiont entry into host cell / virion attachment to host cell
Similarity search - Function
Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / 3 Solenoid / Pectin lyase fold / Pectin lyase fold/virulence factor / Mainly Beta
Similarity search - Domain/homology
Putative pectin lyase
Similarity search - Component
Biological speciesGeobacillus virus E2
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.008 Å
AuthorsGong, Y.
CitationJournal: Int.J.Biol.Macromol. / Year: 2020
Title: Structural and functional characterization of the deep-sea thermophilic bacteriophage GVE2 tailspike protein.
Authors: Zhang, L. / Yan, Y. / Gan, Q. / She, Z. / Zhu, K. / Wang, J. / Gao, Z. / Dong, Y. / Gong, Y.
History
DepositionJul 6, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative pectin lyase
B: Putative pectin lyase
C: Putative pectin lyase


Theoretical massNumber of molelcules
Total (without water)170,0883
Polymers170,0883
Non-polymers00
Water23,8881326
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24000 Å2
ΔGint-161 kcal/mol
Surface area47460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.842, 150.808, 84.707
Angle α, β, γ (deg.)90.000, 95.140, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative pectin lyase


Mass: 56695.992 Da / Num. of mol.: 3 / Fragment: tail spike protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus virus E2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A6M964
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1326 / 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: 2.39 Å3/Da / Density % sol: 48.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M HEPES, 0.2M sodium chloride, pH 7.5, 25% (w/v) polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→36.7 Å / Num. obs: 101736 / % possible obs: 95.8 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 16.9
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.54 / Num. unique obs: 2846

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.008→36.698 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 20.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1958 5077 4.99 %
Rwork0.158 96659 -
obs0.1598 101736 95.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.53 Å2 / Biso mean: 23.2745 Å2 / Biso min: 5.63 Å2
Refinement stepCycle: final / Resolution: 2.008→36.698 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11910 0 0 1326 13236
Biso mean---31.03 -
Num. residues----1551
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.008-2.03060.2241410.1716278683
2.0306-2.05450.23211620.1676331799
2.0545-2.07950.19931860.1702329099
2.0795-2.10580.22221820.1676329598
2.1058-2.13350.20741720.1625328598
2.1335-2.16280.2241620.1551333399
2.1628-2.19360.21961730.1645329198
2.1936-2.22640.27921450.1936320496
2.2264-2.26120.40161040.3154201460
2.2612-2.29820.24121840.1872308192
2.2982-2.33790.21191720.1544330999
2.3379-2.38040.19341790.1508326298
2.3804-2.42610.18711610.15328598
2.4261-2.47570.22781480.1536335099
2.4757-2.52950.21681820.1593330699
2.5295-2.58830.24161900.1602325798
2.5883-2.6530.20361700.1627332898
2.653-2.72470.23182060.1602322498
2.7247-2.80490.19481760.1642329598
2.8049-2.89540.20341940.1631333698
2.8954-2.99880.18681740.1567330299
2.9988-3.11880.18691660.1624332699
3.1188-3.26070.20951780.1643335499
3.2607-3.43250.17971750.1543330999
3.4325-3.64730.16621620.1433328297
3.6473-3.92860.17861440.1544282384
3.9286-4.32340.13811670.1196323696
4.3234-4.94780.1331690.1153396100
4.9478-6.22870.17591730.15823365100
6.2287-36.6980.18151800.173341899

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