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- PDB-5x5v: Crystal structure of pseudorabies virus glycoprotein D -

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Basic information

Entry
Database: PDB / ID: 5x5v
TitleCrystal structure of pseudorabies virus glycoprotein D
ComponentsGD
KeywordsVIRAL PROTEIN / herpes simplex virus / pseudorabies virus / glycoprotein D
Function / homologyHerpesvirus glycoprotein D/GG/GX domain / Herpesvirus glycoprotein D/GG/GX domain / Immunoglobulin-like domain superfamily / membrane / GD
Function and homology information
Biological speciesSuid herpesvirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLi, A. / Lu, G. / Qi, J. / Wu, L. / Tian, K. / Luo, T. / Shi, Y. / Yan, J. / Gao, G.F.
CitationJournal: To Be Published
Title: Crystal structure of pseudorabies virus glycoprotein D
Authors: Li, A. / Lu, G. / Qi, J. / Wu, L. / Tian, K. / Luo, T. / Shi, Y. / Yan, J. / Gao, G.F.
History
DepositionFeb 17, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GD


Theoretical massNumber of molelcules
Total (without water)44,5851
Polymers44,5851
Non-polymers00
Water6,017334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12610 Å2
2
A: GD

A: GD


Theoretical massNumber of molelcules
Total (without water)89,1702
Polymers89,1702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_658-x+1,y,-z+31
Buried area2450 Å2
ΔGint-13 kcal/mol
Surface area22770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.398, 60.975, 60.681
Angle α, β, γ (deg.)90.00, 111.22, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-519-

HOH

21A-711-

HOH

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Components

#1: Protein GD / glycoprotein D


Mass: 44584.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Suid herpesvirus 1 / Strain: Becker / Gene: US6 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: G3G933
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.54 Å3/Da / Density % sol: 19.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M ammonium acetate 0.1 M bis-tris pH 5.5 17 % PEG 10,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 42212 / % possible obs: 97.6 % / Redundancy: 6.1 % / Net I/σ(I): 25.5
Reflection shellResolution: 1.5→1.55 Å / CC1/2: 0.966 / Rpim(I) all: 0.129

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C36

2c36


Resolution: 1.5→23.531 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.46
RfactorNum. reflection% reflection
Rfree0.1923 2130 5.05 %
Rwork0.1691 --
obs0.1703 42206 97.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→23.531 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1925 0 0 334 2259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062006
X-RAY DIFFRACTIONf_angle_d1.092743
X-RAY DIFFRACTIONf_dihedral_angle_d12.406738
X-RAY DIFFRACTIONf_chiral_restr0.042281
X-RAY DIFFRACTIONf_plane_restr0.006362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.53490.23261270.19592635X-RAY DIFFRACTION96
1.5349-1.57330.18631030.17912669X-RAY DIFFRACTION97
1.5733-1.61580.19281320.182697X-RAY DIFFRACTION97
1.6158-1.66330.19021490.17052620X-RAY DIFFRACTION97
1.6633-1.7170.20471310.16922676X-RAY DIFFRACTION97
1.717-1.77830.19561450.16812655X-RAY DIFFRACTION98
1.7783-1.84950.18521370.17372712X-RAY DIFFRACTION98
1.8495-1.93370.2151410.17432654X-RAY DIFFRACTION98
1.9337-2.03550.2421530.16662675X-RAY DIFFRACTION98
2.0355-2.1630.17831530.16152704X-RAY DIFFRACTION99
2.163-2.32990.18231510.17122702X-RAY DIFFRACTION99
2.3299-2.56410.20271560.16862709X-RAY DIFFRACTION99
2.5641-2.93450.21691690.17862711X-RAY DIFFRACTION99
2.9345-3.69490.17461370.16362740X-RAY DIFFRACTION99
3.6949-23.53360.17531460.16472517X-RAY DIFFRACTION90
Refinement TLS params.Method: refined / Origin x: -4.1506 Å / Origin y: -67.6526 Å / Origin z: 71.3213 Å
111213212223313233
T0.1185 Å20.0096 Å2-0.0031 Å2-0.0981 Å2-0.0083 Å2--0.1104 Å2
L1.144 °2-0.0101 °20.1049 °2-0.5552 °2-0.0955 °2--0.8134 °2
S0.0476 Å °0.1345 Å °0.0031 Å °-0.0318 Å °-0.0532 Å °0.0552 Å °0.012 Å °-0.0111 Å °0.0008 Å °
Refinement TLS groupSelection details: all

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