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- PDB-1ce0: TRIMERIZATION SPECIFICITY IN HIV-1 GP41: ANALYSIS WITH A GCN4 LEU... -

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Basic information

Entry
Database: PDB / ID: 1ce0
TitleTRIMERIZATION SPECIFICITY IN HIV-1 GP41: ANALYSIS WITH A GCN4 LEUCINE ZIPPER MODEL
ComponentsPROTEIN (LEUCINE ZIPPER MODEL H38-P1)
KeywordsHIV-1 ENVELOPE PROTEIN / GP41 / PROTEIN OLIGOMERIZATION / COILED COIL / LEUCINE ZIPPER
Function / homology:
Function and homology information
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsShu, W. / Ji, H. / Lu, M.
Citation
Journal: Biochemistry / Year: 1999
Title: Trimerization specificity in HIV-1 gp41: analysis with a GCN4 leucine zipper model.
Authors: Shu, W. / Ji, H. / Lu, M.
#1: Journal: Science / Year: 1991
Title: X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil.
Authors: O'Shea, E.K. / Klemm, J.D. / Kim, P.S. / Alber, T.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: Atomic structure of a thermostable subdomain of HIV-1 gp41.
Authors: Tan, K. / Liu, J. / Wang, J. / Shen, S. / Lu, M.
History
DepositionMar 12, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 19, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.4Aug 9, 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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (LEUCINE ZIPPER MODEL H38-P1)
B: PROTEIN (LEUCINE ZIPPER MODEL H38-P1)
C: PROTEIN (LEUCINE ZIPPER MODEL H38-P1)


Theoretical massNumber of molelcules
Total (without water)13,5883
Polymers13,5883
Non-polymers00
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-32 kcal/mol
Surface area6720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.785, 50.785, 119.251
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Cell settinghexagonal
Space group name H-MP61

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Components

#1: Protein/peptide PROTEIN (LEUCINE ZIPPER MODEL H38-P1)


Mass: 4529.289 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Description: SYNTHETIC GENE / Plasmid: PH38-P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(PLYS) / References: UniProt: Q7SIH0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 3.27 Å3/Da / Density % sol: 69.7 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17 mg/mlprotein1drop
20.1 MHEPES1drop
31.5 M1dropLi2SO4
420 %(v/v)glycerol1drop
520 %(v/v)glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.978
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 1998 / Details: REFOCUSSING MIRROR, RH WORKING SURFACE
RadiationMonochromator: DOUBLE-CRYSTAL, FIXED-EXIT SI-III MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 6765 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 20.4
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.097 / Mean I/σ(I) obs: 10.5 / Rsym value: 0.097 / % possible all: 99.8
Reflection
*PLUS
Num. measured all: 22836

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GCM

1gcm


Resolution: 2.4→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.294 500 7 %RANDOM
Rwork0.221 ---
obs-6559 95.8 %-
Displacement parametersBiso mean: 37.5 Å2
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms895 0 0 78 973
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.303
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.516
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 7 % / Rfactor obs: 0.221
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 37.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.516

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