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- PDB-2zfc: X-ray crystal structure of an engineered N-terminal HIV-1 GP41 tr... -

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Basic information

Entry
Database: PDB / ID: 2zfc
TitleX-ray crystal structure of an engineered N-terminal HIV-1 GP41 trimer with enhanced stability and potency
ComponentsHIV-1 GP41
KeywordsVIRAL PROTEIN / hiv-1 / gp41
Function / homologySingle alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Function and homology information
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.5 Å
AuthorsDwyer, J.J. / Wilson, K.L. / Martin, K. / Seedorff, J.E. / Hasan, A. / Kim, H.
CitationJournal: Protein Sci. / Year: 2008
Title: Design of an engineered N-terminal HIV-1 gp41 trimer with enhanced stability and potency
Authors: Dwyer, J.J. / Wilson, K.L. / Martin, K. / Seedorff, J.E. / Hasan, A. / Medinas, R.J. / Davison, D.K. / Feese, M.D. / Richter, H.T. / Kim, H. / Matthews, T.J. / Delmedico, M.K.
History
DepositionDec 29, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Mar 13, 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

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Assembly

Deposited unit
A: HIV-1 GP41
B: HIV-1 GP41
C: HIV-1 GP41


Theoretical massNumber of molelcules
Total (without water)16,6753
Polymers16,6753
Non-polymers00
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-44.4 kcal/mol
Surface area8660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.569, 103.569, 44.895
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein/peptide HIV-1 GP41


Mass: 5558.464 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: synthetic peptide
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.78 Å3/Da / Density % sol: 55.74 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 10%(v/v) iso-propanol, 0.1M Na Citrate pH 5.6, 10%(w/v) PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Details: Osmic Blue
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 28563 / % possible obs: 95.5 % / Redundancy: 5 % / Biso Wilson estimate: 24.9 Å2 / Rsym value: 0.046 / Net I/σ(I): 44
Reflection shellResolution: 1.5→1.55 Å / Mean I/σ(I) obs: 1.6 / Rsym value: 0.312 / % possible all: 68.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
PDB_EXTRACT3.004data extraction
StructureStudiodata collection
REFMACrefinement
RefinementMethod to determine structure: SAD / Resolution: 1.5→20 Å /
RfactorNum. reflection
Rfree0.266 -
Rwork0.221 -
obs-28563
Displacement parametersBiso mean: 27.739 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1046 0 0 185 1231
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.015
X-RAY DIFFRACTIONp_angle_d0.9
LS refinement shellHighest resolution: 1.5 Å / Rfactor Rfree: 0.266 / Rfactor Rwork: 0.221

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