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- PDB-4hlr: Structural Determinants of Trimerization Specificity in HIV-1 gp4... -

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Basic information

Entry
Database: PDB / ID: 4hlr
TitleStructural Determinants of Trimerization Specificity in HIV-1 gp41 Protein
ComponentsGp41
KeywordsVIRAL PROTEIN / gp41 / HIV-1 / trimerization domain / oligomeric structure
Function / homologyRetroviral envelope protein / Retroviral envelope protein GP41-like / host cell plasma membrane / virion membrane / structural molecule activity / plasma membrane / HEXANE-1,6-DIOL / Env polyprotein
Function and homology information
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsLiu, J. / Lu, M.
CitationJournal: To be Published
Title: Structural Determinants of Trimerization Specificity in HIV-1 gp41 Protein
Authors: Liu, J. / Li, Q. / Dey, A.K. / Moore, J.P. / Lu, M.
History
DepositionOct 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gp41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,0552
Polymers3,9371
Non-polymers1181
Water84747
1
A: Gp41
hetero molecules

A: Gp41
hetero molecules

A: Gp41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1646
Polymers11,8103
Non-polymers3553
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area3380 Å2
ΔGint-29 kcal/mol
Surface area7900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.347, 45.347, 42.091
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein/peptide Gp41 /


Mass: 3936.581 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN / Mutation: I14L, L17I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Escherichia coli (E. coli) / References: UniProt: Q9YYZ1
#2: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL / 1,6-Hexanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 3.17 Å3/Da / Density % sol: 61.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 2.5M 1,6-Hexanediol, 0.1M Sodium Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97907 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 1.57→42.1 Å / Num. all: 6325 / Num. obs: 6325 / % possible obs: 87.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 21.1 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 15.9
Reflection shellResolution: 1.57→1.63 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 5.6 / Num. unique all: 692 / % possible all: 96.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3U91

3u91


Resolution: 1.57→42.09 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.149 / SU ML: 0.057 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24003 604 9.5 %RANDOM
Rwork0.19355 ---
obs0.19786 6325 87.9 %-
all-6325 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.957 Å2
Baniso -1Baniso -2Baniso -3
1-1.6 Å20.8 Å20 Å2
2--1.6 Å20 Å2
3----2.39 Å2
Refinement stepCycle: LAST / Resolution: 1.57→42.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms264 0 8 47 319
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.02274
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3131.982366
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.276530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.9852514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.0811555
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.421152
X-RAY DIFFRACTIONr_chiral_restr0.1470.242
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02194
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.57→1.612 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 43 -
Rwork0.312 410 -
obs-453 94.97 %
Refinement TLS params.Method: refined / Origin x: -21.247 Å / Origin y: 7.011 Å / Origin z: 11.626 Å
111213212223313233
T0.0719 Å20.0282 Å20.0053 Å2-0.0176 Å20.0128 Å2--0.045 Å2
L0.3028 °20.0757 °2-1.0561 °2-0.1971 °2-0.3863 °2--8.0528 °2
S0.0156 Å °0.0148 Å °0.0427 Å °-0.0185 Å °-0.0236 Å °0.001 Å °0.4228 Å °0.2 Å °0.008 Å °

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