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- PDB-4dzu: Complex of 3-alpha bound to gp41-5 -

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Basic information

Entry
Database: PDB / ID: 4dzu
TitleComplex of 3-alpha bound to gp41-5
Components
  • 3-alpha
  • gp41-5
KeywordsDE NOVO PROTEIN / viral fusion
Biological speciesSynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJohnson, L.M. / Mortenson, D.E. / Yun, H.G. / Horne, W.S. / Ketas, T.J. / Lu, M. / Moore, J.P. / Gellman, S.H.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: Enhancement of alpha-helix mimicry by an alpha / beta-peptide foldamer via incorporation of a dense ionic side-chain array.
Authors: Johnson, L.M. / Mortenson, D.E. / Yun, H.G. / Horne, W.S. / Ketas, T.J. / Lu, M. / Moore, J.P. / Gellman, S.H.
History
DepositionMar 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: gp41-5
B: 3-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1043
Polymers27,0122
Non-polymers921
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-20 kcal/mol
Surface area11140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.293, 121.208, 59.259
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein gp41-5


Mass: 22246.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein/peptide 3-alpha


Mass: 4765.263 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.57 Å3/Da / Density % sol: 52.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, 1.0 M ammonium sulfate, 25% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 17, 2010
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.1→42.41 Å / Num. obs: 16616 / % possible obs: 99.9 % / Redundancy: 5.9 % / Rsym value: 0.063 / Χ2: 0.934 / Net I/σ(I): 15.95
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allRsym valueΧ2Diffraction-ID% possible all
2.1-2.1468100.2670.9511100
2.14-2.1868300.20.9681100
2.18-2.2268160.1960.9431100
2.22-2.265.98090.2241.0291100
2.26-2.3168200.1670.9561100
2.31-2.3768140.1330.9891100
2.37-2.4268240.1160.9711100
2.42-2.4968150.1010.9071100
2.49-2.5668340.0910.9431100
2.56-2.6568010.080.9791100
2.65-2.7468350.0830.9741100
2.74-2.8568260.0650.9841100
2.85-2.9868360.0571.0181100
2.98-3.1468320.0590.9651100
3.14-3.3368230.0640.7481100
3.33-3.595.98440.0740.8771100
3.59-3.955.98420.080.9051100
3.95-4.525.98400.0620.9671100
4.52-5.75.88600.0390.9521100
5.7-505.39050.0360.648198.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.7.0009refinement
PDB_EXTRACT3.1data extraction
EMBLMD-2data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→42.4 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.83 / SU ML: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.214 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2497 837 5 %RANDOM
Rwork0.2135 ---
obs0.2153 16599 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 101.91 Å2 / Biso mean: 46.8869 Å2 / Biso min: 25.78 Å2
Baniso -1Baniso -2Baniso -3
1-7.23 Å20 Å2-0 Å2
2---3.23 Å2-0 Å2
3----4.01 Å2
Refine analyzeLuzzati coordinate error obs: 0.299 Å
Refinement stepCycle: LAST / Resolution: 2.1→42.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1791 0 6 30 1827
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191833
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.9252476
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4885225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.81326.3100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.09915337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9031510
X-RAY DIFFRACTIONr_chiral_restr0.1120.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021386
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 50 -
Rwork0.291 1132 -
all-1182 -
obs--97.2 %

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