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- PDB-8w52: p17 protein structure of HIV2 when OLA1 existing -

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Basic information

Entry
Database: PDB / ID: 8w52
Titlep17 protein structure of HIV2 when OLA1 existing
ComponentsGag polyprotein
KeywordsVIRAL PROTEIN / HIV2 / Matrix / p17 / Gag
Function / homology
Function and homology information


viral budding via host ESCRT complex / host multivesicular body / viral nucleocapsid / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / RNA binding / zinc ion binding / membrane
Similarity search - Function
Retroviral nucleocapsid Gag protein p24, N-terminal / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal ...Retroviral nucleocapsid Gag protein p24, N-terminal / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus type 2 subtype A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsDang, L.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: p17 protein structure of HIV2 when OLA1 existing
Authors: Dang, L.L.
History
DepositionAug 25, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gag polyprotein
B: Gag polyprotein
C: Gag polyprotein
D: Gag polyprotein
E: Gag polyprotein
F: Gag polyprotein
G: Gag polyprotein
H: Gag polyprotein
I: Gag polyprotein
J: Gag polyprotein
K: Gag polyprotein
L: Gag polyprotein
M: Gag polyprotein
N: Gag polyprotein
O: Gag polyprotein
P: Gag polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,19436
Polymers241,27216
Non-polymers1,92120
Water6,053336
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.780, 123.780, 108.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221
Space group name HallP2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11M-213-

HOH

21O-212-

HOH

31P-310-

HOH

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Components

#1: Protein
Gag polyprotein / Pr55Gag


Mass: 15079.520 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 2 subtype A (isolate BEN)
Gene: gag / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P18095
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.14 Å3/Da / Density % sol: 42.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.2M (NH4)2SO4 0.1M BISTris pH=5.5 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.38→46.19 Å / Num. obs: 67420 / % possible obs: 99.79 % / Redundancy: 13.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.08144 / Net I/σ(I): 19.85
Reflection shellResolution: 2.381→2.466 Å / Num. unique obs: 85812 / CC1/2: 0.974

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→46.19 Å / Cross valid method: FREE R-VALUE / σ(F): 108.15 / Phase error: 32.7313
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.248 3373 5 %
Rwork0.2101 64047 -
obs0.2245 67420 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.83 Å2
Refinement stepCycle: LAST / Resolution: 2.38→46.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13667 0 100 336 14103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002413938
X-RAY DIFFRACTIONf_angle_d0.526718687
X-RAY DIFFRACTIONf_chiral_restr0.03582117
X-RAY DIFFRACTIONf_plane_restr0.00452321
X-RAY DIFFRACTIONf_dihedral_angle_d19.29345425
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.420.36061600.31863049X-RAY DIFFRACTION91.62
2.42-2.470.34441650.31613142X-RAY DIFFRACTION95.01
2.47-2.510.34271680.31263183X-RAY DIFFRACTION94.99
2.51-2.560.33351660.30143161X-RAY DIFFRACTION95.01
2.57-2.620.34341650.29353139X-RAY DIFFRACTION95.01
2.62-2.680.36221690.2893200X-RAY DIFFRACTION94.98
2.68-2.750.34361690.29613218X-RAY DIFFRACTION95.01
2.75-2.820.28641660.27353139X-RAY DIFFRACTION94.98
2.82-2.910.31041670.2743177X-RAY DIFFRACTION95.01
2.91-30.29271670.26453186X-RAY DIFFRACTION95.02
3-3.110.29171700.25083229X-RAY DIFFRACTION95
3.11-3.230.28571670.23843174X-RAY DIFFRACTION94.94
3.23-3.380.26841690.21673207X-RAY DIFFRACTION94.99
3.38-3.560.2521680.2083198X-RAY DIFFRACTION95.01
3.56-3.780.23871680.18363177X-RAY DIFFRACTION94.98
3.78-4.070.21551710.17653252X-RAY DIFFRACTION95
4.07-4.480.20171700.16713225X-RAY DIFFRACTION94.94
4.48-5.130.21721710.16443265X-RAY DIFFRACTION95.02
5.13-6.460.23731740.2313291X-RAY DIFFRACTION94.98
6.46-46.190.21271810.20593437X-RAY DIFFRACTION94.89

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