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- PDB-3lef: Crystal structure of HIV epitope-scaffold 4E10_S0_1Z6NA_001 -

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Basic information

Entry
Database: PDB / ID: 3lef
TitleCrystal structure of HIV epitope-scaffold 4E10_S0_1Z6NA_001
ComponentsUncharacterized protein 4E10_S0_1Z6NA_001 (T18)
KeywordsIMMUNE SYSTEM / EPITOPE-SCAFFOLD
Function / homologyGlutaredoxin / Glutaredoxin / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesARTIFICIAL GENE (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHolmes, M.A.
CitationJournal: Structure / Year: 2010
Title: Computational Design of Epitope-Scaffolds Allows Induction of Antibodies Specific for a Poorly Immunogenic HIV Vaccine Epitope.
Authors: Correia, B.E. / Ban, Y.E. / Holmes, M.A. / Xu, H. / Ellingson, K. / Kraft, Z. / Carrico, C. / Boni, E. / Sather, D.N. / Zenobia, C. / Burke, K.Y. / Bradley-Hewitt, T. / Bruhn-Johannsen, J.F. ...Authors: Correia, B.E. / Ban, Y.E. / Holmes, M.A. / Xu, H. / Ellingson, K. / Kraft, Z. / Carrico, C. / Boni, E. / Sather, D.N. / Zenobia, C. / Burke, K.Y. / Bradley-Hewitt, T. / Bruhn-Johannsen, J.F. / Kalyuzhniy, O. / Baker, D. / Strong, R.K. / Stamatatos, L. / Schief, W.R.
History
DepositionJan 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_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

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Assembly

Deposited unit
A: Uncharacterized protein 4E10_S0_1Z6NA_001 (T18)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4122
Polymers19,3501
Non-polymers621
Water99155
1
A: Uncharacterized protein 4E10_S0_1Z6NA_001 (T18)
hetero molecules

A: Uncharacterized protein 4E10_S0_1Z6NA_001 (T18)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8244
Polymers38,7002
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area1740 Å2
ΔGint-0 kcal/mol
Surface area14870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.41, 56.41, 324.13
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-223-

HOH

21A-224-

HOH

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Components

#1: Protein Uncharacterized protein 4E10_S0_1Z6NA_001 (T18)


Mass: 19350.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The epitope-scaffold is based on the hypothetical protein PA1234 from Pseudomonas aeruginosa (PDB ID 1Z6N)
Source: (gene. exp.) ARTIFICIAL GENE (others) / Plasmid: PET29 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) STAR
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 3.85 Å3/Da / Density % sol: 68.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Na/K tartrate, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 107 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 17, 2007 / Details: Rigaku Varimax HR
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→48.3 Å / Num. all: 13770 / Num. obs: 13770 / % possible obs: 93.7 % / Redundancy: 8.4 % / Biso Wilson estimate: 56.3 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.83 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 3.9 / Num. unique all: 1304 / % possible all: 91.5

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.2.0019refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Computationally-derived model of the epitope-scaffold, based on 1Z6N

1z6n


Resolution: 2.3→46.78 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.937 / SU B: 15.538 / SU ML: 0.189 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29042 667 4.9 %RANDOM
Rwork0.25831 ---
obs0.25978 13064 93.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.573 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å2-0.11 Å20 Å2
2---0.22 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1261 0 4 55 1320
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221302
X-RAY DIFFRACTIONr_bond_other_d0.0010.02875
X-RAY DIFFRACTIONr_angle_refined_deg1.1461.9691766
X-RAY DIFFRACTIONr_angle_other_deg0.78132124
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.955168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.95123.96863
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.25915212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9051511
X-RAY DIFFRACTIONr_chiral_restr0.070.2200
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021484
X-RAY DIFFRACTIONr_gen_planes_other00.02273
X-RAY DIFFRACTIONr_nbd_refined0.2030.3265
X-RAY DIFFRACTIONr_nbd_other0.2030.3908
X-RAY DIFFRACTIONr_nbtor_refined0.180.5621
X-RAY DIFFRACTIONr_nbtor_other0.0910.5702
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.581
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0980.36
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2140.323
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.54
X-RAY DIFFRACTIONr_mcbond_it0.6662886
X-RAY DIFFRACTIONr_mcbond_other0.1332340
X-RAY DIFFRACTIONr_mcangle_it1.03531300
X-RAY DIFFRACTIONr_scbond_it1.6624514
X-RAY DIFFRACTIONr_scangle_it2.5476464
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 49 -
Rwork0.346 905 -
obs--89.92 %

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