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- PDB-8ipg: Structure of HP101/N44 -

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Basic information

Entry
Database: PDB / ID: 8ipg
TitleStructure of HP101/N44
Components
  • Env polyprotein (Fragment)
  • HP101
KeywordsVIRAL PROTEIN / HIV / envelope / 6HB
Function / homologyRetroviral envelope protein / Retroviral envelope protein GP41-like / viral envelope / host cell plasma membrane / structural molecule activity / virion membrane / plasma membrane / Env polyprotein
Function and homology information
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsLiu, N. / Qin, B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of HP101/N44
Authors: Liu, N. / Qin, B.
History
DepositionMar 14, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Env polyprotein (Fragment)
B: Env polyprotein (Fragment)
C: Env polyprotein (Fragment)
D: HP101
E: HP101
F: HP101


Theoretical massNumber of molelcules
Total (without water)27,0826
Polymers27,0826
Non-polymers00
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12440 Å2
ΔGint-100 kcal/mol
Surface area12020 Å2
MethodPISA
2
A: Env polyprotein (Fragment)
F: HP101


Theoretical massNumber of molelcules
Total (without water)9,0272
Polymers9,0272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-11 kcal/mol
Surface area6520 Å2
MethodPISA
3
B: Env polyprotein (Fragment)
D: HP101


Theoretical massNumber of molelcules
Total (without water)9,0272
Polymers9,0272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-11 kcal/mol
Surface area6530 Å2
MethodPISA
4
C: Env polyprotein (Fragment)
E: HP101


Theoretical massNumber of molelcules
Total (without water)9,0272
Polymers9,0272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-12 kcal/mol
Surface area6820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.387, 41.609, 85.309
Angle α, β, γ (deg.)90.00, 109.69, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11F-123-

GLU

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Components

#1: Protein/peptide Env polyprotein (Fragment)


Mass: 5037.884 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: W8QBL2
#2: Protein/peptide HP101


Mass: 3989.579 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.2 Å3/Da / Density % sol: 44.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG 3350, 0.2M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 7, 2022
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.639→40.161 Å / Num. obs: 56809 / % possible obs: 97.3 % / Redundancy: 3.347 % / CC1/2: 0.985 / Rmerge(I) obs: 0.125 / Net I/σ(I): 5.27
Reflection shellResolution: 1.639→1.74 Å / Redundancy: 2.835 % / Rmerge(I) obs: 1.049 / Num. unique obs: 9187 / CC1/2: 0.447 / % possible all: 91.7

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→40.16 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 29.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.288 1429 5.01 %
Rwork0.2468 --
obs0.2488 28545 97.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.64→40.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1867 0 0 108 1975
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071853
X-RAY DIFFRACTIONf_angle_d0.9442464
X-RAY DIFFRACTIONf_dihedral_angle_d3.949228
X-RAY DIFFRACTIONf_chiral_restr0.045286
X-RAY DIFFRACTIONf_plane_restr0.008315
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.70.3821280.34172414X-RAY DIFFRACTION88
1.7-1.770.32551430.29962721X-RAY DIFFRACTION99
1.77-1.850.31631450.28382745X-RAY DIFFRACTION99
1.85-1.940.30271430.27722727X-RAY DIFFRACTION98
1.94-2.060.34151440.2622728X-RAY DIFFRACTION98
2.07-2.220.25141420.232702X-RAY DIFFRACTION99
2.22-2.450.2651470.23112786X-RAY DIFFRACTION100
2.45-2.80.26891430.23942723X-RAY DIFFRACTION99
2.8-3.530.28561450.24032748X-RAY DIFFRACTION98
3.53-40.160.29461490.24342822X-RAY DIFFRACTION98

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