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- PDB-3wmi: Crystal structure of EIAV wild type gp45 -

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Basic information

Entry
Database: PDB / ID: 3wmi
TitleCrystal structure of EIAV wild type gp45
Components(EIAV gp45 wild type) x 2
KeywordsVIRAL PROTEIN / alpha-helix / virus fusion
Function / homology
Function and homology information


viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane
Similarity search - Function
Gp90 envelope polyprotein of equine infectious anemia virus (EIAV) / EIAV coat protein, gp90 / Retroviral envelope protein / Retroviral envelope protein GP41-like
Similarity search - Domain/homology
Envelope glycoprotein
Similarity search - Component
Biological speciesEquine (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLiu, X. / Du, J. / Qiao, W.
CitationJournal: To be Published
Title: A mutation associated with EIAV vaccine strain within heptad repeat of EIAV gp45 provides insight into vaccine development for HIV
Authors: Liu, X. / Du, J. / Qiao, W.
History
DepositionNov 19, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 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: EIAV gp45 wild type
B: EIAV gp45 wild type


Theoretical massNumber of molelcules
Total (without water)11,0292
Polymers11,0292
Non-polymers00
Water3,297183
1
A: EIAV gp45 wild type
B: EIAV gp45 wild type

A: EIAV gp45 wild type
B: EIAV gp45 wild type

A: EIAV gp45 wild type
B: EIAV gp45 wild type


Theoretical massNumber of molelcules
Total (without water)33,0876
Polymers33,0876
Non-polymers00
Water1086
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 area13170 Å2
ΔGint-124 kcal/mol
Surface area14570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.051, 47.051, 101.918
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-604-

HOH

21A-608-

HOH

31A-624-

HOH

41A-644-

HOH

51A-654-

HOH

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Components

#1: Protein EIAV gp45 wild type


Mass: 6578.155 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equine (horse) / Production host: Escherichia coli (E. coli) / References: UniProt: E2E2L9*PLUS
#2: Protein/peptide EIAV gp45 wild type


Mass: 4450.874 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equine (horse) / Production host: Escherichia coli (E. coli) / References: UniProt: E2E2L9*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION. THE MUTATION OF THE GP45 IN POSITION 505, IN WILD TYPE IS 505VAL AND IN VACCINE IS 505THR.

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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: 2.95 Å3/Da / Density % sol: 58.34 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 5.5
Details: 0.1M Bis-Tris, 2M NaCl, pH 5.5, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9794 Å
DetectorType: ENRAF-NONIUS / Detector: CCD / Date: May 9, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.9→31.824 Å / Num. obs: 10074 / % possible obs: 11 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2.9
Reflection shellResolution: 1.9→1.93 Å / % possible all: 95

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Processing

Software
NameVersionClassification
HKL-2000data collection
CNSrefinement
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→31.824 Å / SU ML: 0.24 / σ(F): 1.4 / Phase error: 23.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2292 481 4.8 %RANDOM
Rwork0.1754 ---
all0.1783 ---
obs0.1778 10028 99.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→31.824 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms773 0 0 183 956
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007785
X-RAY DIFFRACTIONf_angle_d0.7881068
X-RAY DIFFRACTIONf_dihedral_angle_d17.691279
X-RAY DIFFRACTIONf_chiral_restr0.061125
X-RAY DIFFRACTIONf_plane_restr0.003140
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-2.17520.2271690.1712315399
2.1752-2.74030.22011690.17913161100
2.7403-31.82880.23571430.1747323399

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