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- PDB-7ff1: Structure of C34E136G/N36 -

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Basic information

Entry
Database: PDB / ID: 7ff1
TitleStructure of C34E136G/N36
Components
  • gp41 C34E136G
  • gp41 N36
KeywordsVIRAL PROTEIN / HIV / envlope / 6HB
Function / homologyRetroviral envelope protein / Retroviral envelope protein GP41-like / viral envelope / host cell plasma membrane / virion membrane / structural molecule activity / plasma membrane / Env polyprotein
Function and homology information
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.689 Å
AuthorsYu, D.W. / Qin, B.
CitationJournal: To Be Published
Title: Structure of C34E136G/N36
Authors: Yu, D.W. / Qin, B.
History
DepositionJul 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.3Mar 12, 2025Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.content_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
N: gp41 N36
C: gp41 C34E136G
B: gp41 N36
A: gp41 C34E136G
E: gp41 N36
D: gp41 C34E136G


Theoretical massNumber of molelcules
Total (without water)25,0756
Polymers25,0756
Non-polymers00
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12240 Å2
ΔGint-102 kcal/mol
Surface area10420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.089, 50.391, 56.909
Angle α, β, γ (deg.)90.000, 90.130, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-724-

HOH

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Components

#1: Protein/peptide gp41 N36


Mass: 4152.843 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: C7F357
#2: Protein/peptide gp41 C34E136G


Mass: 4205.553 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.: 133 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.52 Å3/Da / Density % sol: 51.16 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: BIS-Tris,Polyethylene glycol monomethyl ether 5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.689→43.74 Å / Num. obs: 28119 / % possible obs: 99.7 % / Redundancy: 6.628 % / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Net I/σ(I): 19.95
Reflection shellResolution: 1.689→1.79 Å / Rmerge(I) obs: 0.976 / Mean I/σ(I) obs: 1.45 / Num. unique obs: 4478 / CC1/2: 0.757 / % possible all: 99.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AIK

1aik


Resolution: 1.689→43.74 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2239 1271 4.53 %
Rwork0.2158 26760 -
obs0.2162 28031 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.85 Å2 / Biso mean: 44.4355 Å2 / Biso min: 24.97 Å2
Refinement stepCycle: final / Resolution: 1.689→43.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1767 0 0 133 1900
Biso mean---48.77 -
Num. residues----210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.031788
X-RAY DIFFRACTIONf_angle_d1.4012412
X-RAY DIFFRACTIONf_chiral_restr0.132267
X-RAY DIFFRACTIONf_plane_restr0.014315
X-RAY DIFFRACTIONf_dihedral_angle_d19.3211080
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6891-1.75670.39161510.32892915100
1.7567-1.83670.31071220.28982977100
1.8367-1.93350.31081400.26982965100
1.9335-2.05460.33971250.27142970100
2.0546-2.21330.21441250.21442985100
2.2133-2.4360.25661490.23472984100
2.436-2.78840.24191190.23252991100
2.7884-3.51290.21211710.20942964100
3.5129-43.740.1991690.1893300999

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