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- PDB-3tih: Crystal structure of unliganded HIV-1 clade C strain ZM109F.PB4 g... -

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Basic information

Entry
Database: PDB / ID: 3tih
TitleCrystal structure of unliganded HIV-1 clade C strain ZM109F.PB4 gp120 core
ComponentsHIV-1 clade C ZM109F.PB4 gp120
KeywordsVIRAL PROTEIN / HIV-1 gp120 / unliganded / clade C ZM109F.PB4
Function / homologyHIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Beta Complex / Mainly Beta
Function and homology information
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsKwon, Y.D. / Kwong, P.D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Unliganded HIV-1 gp120 core structures assume the CD4-bound conformation with regulation by quaternary interactions and variable loops.
Authors: Kwon, Y.D. / Finzi, A. / Wu, X. / Dogo-Isonagie, C. / Lee, L.K. / Moore, L.R. / Schmidt, S.D. / Stuckey, J. / Yang, Y. / Zhou, T. / Zhu, J. / Vicic, D.A. / Debnath, A.K. / Shapiro, L. / ...Authors: Kwon, Y.D. / Finzi, A. / Wu, X. / Dogo-Isonagie, C. / Lee, L.K. / Moore, L.R. / Schmidt, S.D. / Stuckey, J. / Yang, Y. / Zhou, T. / Zhu, J. / Vicic, D.A. / Debnath, A.K. / Shapiro, L. / Bewley, C.A. / Mascola, J.R. / Sodroski, J.G. / Kwong, P.D.
History
DepositionAug 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Database references
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HIV-1 clade C ZM109F.PB4 gp120
B: HIV-1 clade C ZM109F.PB4 gp120
C: HIV-1 clade C ZM109F.PB4 gp120
D: HIV-1 clade C ZM109F.PB4 gp120


Theoretical massNumber of molelcules
Total (without water)154,1904
Polymers154,1904
Non-polymers00
Water00
1
A: HIV-1 clade C ZM109F.PB4 gp120


Theoretical massNumber of molelcules
Total (without water)38,5481
Polymers38,5481
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HIV-1 clade C ZM109F.PB4 gp120


Theoretical massNumber of molelcules
Total (without water)38,5481
Polymers38,5481
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: HIV-1 clade C ZM109F.PB4 gp120


Theoretical massNumber of molelcules
Total (without water)38,5481
Polymers38,5481
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: HIV-1 clade C ZM109F.PB4 gp120


Theoretical massNumber of molelcules
Total (without water)38,5481
Polymers38,5481
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.574, 197.208, 83.321
Angle α, β, γ (deg.)90.00, 91.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
HIV-1 clade C ZM109F.PB4 gp120


Mass: 38547.570 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: HIV-1 env / Plasmid: pVRC8400 / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
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: 2.96 Å3/Da / Density % sol: 58.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG 3350, 10% iso-propanol, 0.2 M Ammonium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4→50 Å / Num. all: 15241 / Num. obs: 12925 / % possible obs: 84.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.151 / Rsym value: 0.114 / Net I/σ(I): 6.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
4-4.142.50.3452.10.292157.8
4.14-4.312.70.273.10.204166.1
4.31-4.52.90.253.40.206176.3
4.5-4.743.10.23740.185182.7
4.74-5.043.20.224.50.193187.3
5.04-5.433.30.2114.90.189190.2
5.43-5.973.30.2234.90.178191.2
5.97-6.843.50.2115.50.181196.2
6.84-8.63.80.12511.40.111100
8.6-503.70.061260.064199.7

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4→46.695 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 1.23 / σ(F): 1.34 / Phase error: 36.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3122 625 4.87 %
Rwork0.2829 --
obs0.2844 12826 84.63 %
all-15152 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 158.036 Å2 / ksol: 0.33 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-33.6059 Å2-0 Å2-11.8867 Å2
2---42.7126 Å2-0 Å2
3----16.6852 Å2
Refinement stepCycle: LAST / Resolution: 4→46.695 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10252 0 0 0 10252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310770
X-RAY DIFFRACTIONf_angle_d0.60114548
X-RAY DIFFRACTIONf_dihedral_angle_d10.9333976
X-RAY DIFFRACTIONf_chiral_restr0.0471624
X-RAY DIFFRACTIONf_plane_restr0.0031876
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.0001-4.40240.36651070.32252314X-RAY DIFFRACTION64
4.4024-5.03870.31661470.26413026X-RAY DIFFRACTION84
5.0387-6.34580.33011740.29663259X-RAY DIFFRACTION91
6.3458-46.69830.28641970.27173602X-RAY DIFFRACTION100

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