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- PDB-3k9a: Crystal Structure of HIV gp41 with MPER -

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Basic information

Entry
Database: PDB / ID: 3k9a
TitleCrystal Structure of HIV gp41 with MPER
ComponentsHIV glycoprotein gp41
KeywordsVIRAL PROTEIN / HIV / gp41 / membrane proximal external region / MPER
Function / homologyHelix Hairpins - #210 / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Function and homology information
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / Molecular replacement, Br SAD / Resolution: 2.1 Å
AuthorsShi, W. / Han, D. / Habte, H. / Cho, M. / Chance, M.R.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural characterization of HIV gp41 with the membrane-proximal external region
Authors: Shi, W. / Bohon, J. / Han, D.P. / Habte, H. / Qin, Y. / Cho, M.W. / Chance, M.R.
History
DepositionOct 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HIV glycoprotein gp41


Theoretical massNumber of molelcules
Total (without water)12,7221
Polymers12,7221
Non-polymers00
Water34219
1
A: HIV glycoprotein gp41

A: HIV glycoprotein gp41

A: HIV glycoprotein gp41


Theoretical massNumber of molelcules
Total (without water)38,1663
Polymers38,1663
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area5490 Å2
ΔGint-49 kcal/mol
Surface area13510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.588, 50.588, 155.094
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein HIV glycoprotein gp41


Mass: 12722.096 Da / Num. of mol.: 1 / Fragment: gp41 fusion protein / Mutation: HR1+4XGly+HR2+MPER
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: MCON6 / Gene: gp41 / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS IS A FUSION PROTEIN WITH A LINKER GGGGS IN THE MIDDLE AND SIX-RESIDUES HIS TAGS AT THE C-TERMINUS END

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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: 2.25 Å3/Da / Density % sol: 45.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 45% MPD, 0.2 M sodium acetate, 0.1 M Bis-tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.08 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 28, 2009 / Details: monochromator and mirror
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 7537 / % possible obs: 99.8 % / Redundancy: 30 % / Biso Wilson estimate: 40.71 Å2 / Rsym value: 0.074 / Net I/σ(I): 55.8
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 29.9 % / Mean I/σ(I) obs: 6 / Num. unique all: 355 / Rsym value: 0.713 / % possible all: 100

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Processing

Software
NameClassification
CBASSdata collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: Molecular replacement, Br SAD
Starting model: PDB entry 1AIK

1aik


Resolution: 2.1→42.2 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34
RfactorNum. reflection% reflectionSelection details
Rfree0.2488 563 -Random
Rwork0.2451 ---
obs0.2454 7497 99.7 %-
all-7518 --
Displacement parametersBiso mean: 51.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.3604 Å20 Å20 Å2
2---1.3604 Å20 Å2
3---2.7208 Å2
Refinement stepCycle: LAST / Resolution: 2.1→42.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms642 0 0 19 661
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONfond0.003
X-RAY DIFFRACTIONfngle0.594
X-RAY DIFFRACTIONfihedral15.778
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
2.1-2.310.29191330.2199X-RAY DIFFRACTION1810100
2.31-2.640.27691310.1996X-RAY DIFFRACTION1816100
2.64-3.330.23351370.2101X-RAY DIFFRACTION1856100
3.33-42.20.24061620.2732X-RAY DIFFRACTION201599

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