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- PDB-3lf9: Crystal structure of HIV epitope-scaffold 4E10_D0_1IS1A_001_C -

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Basic information

Entry
Database: PDB / ID: 3lf9
TitleCrystal structure of HIV epitope-scaffold 4E10_D0_1IS1A_001_C
Components4E10_D0_1IS1A_001_C (T161)
KeywordsIMMUNE SYSTEM / EPITOPE-SCAFFOLD
Function / homologyRibosome-recycling factor / Topoisomerase I; Chain A, domain 4 / Orthogonal Bundle / Mainly Alpha
Function and homology information
Biological speciesARTIFICIAL GENE (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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 16, 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 / 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

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Assembly

Deposited unit
A: 4E10_D0_1IS1A_001_C (T161)


Theoretical massNumber of molelcules
Total (without water)13,6981
Polymers13,6981
Non-polymers00
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.660, 75.360, 79.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein 4E10_D0_1IS1A_001_C (T161)


Mass: 13697.619 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The epitope scaffold is based on the ribosome recycling factor from Vibrio parahaemolyticus (PDB ID 1IS1)
Source: (gene. exp.) ARTIFICIAL GENE (others) / Plasmid: PET29 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) STAR
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.23 Å3/Da / Density % sol: 44.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, Ca chloride, 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 SATURN 944+ / Detector: CCD / Date: Jun 4, 2008 / Details: Rigaku Varimax HF
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→32.64 Å / Num. all: 8462 / Num. obs: 8462 / % possible obs: 98.3 % / Redundancy: 4.53 % / Biso Wilson estimate: 27.7 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 18.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.66 % / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 4 / Num. unique all: 755 / % possible all: 89.9

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
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 1IS1

1is1


Resolution: 2→27.37 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.917 / SU B: 8.825 / SU ML: 0.137 / Isotropic thermal model: Isotropic with 4 TLS groups / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25969 396 4.7 %RANDOM
Rwork0.20444 ---
obs0.20697 8032 98.17 %-
all-8032 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.398 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 2→27.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms907 0 0 127 1034
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021936
X-RAY DIFFRACTIONr_bond_other_d0.0040.02631
X-RAY DIFFRACTIONr_angle_refined_deg1.0041.9471263
X-RAY DIFFRACTIONr_angle_other_deg0.84131550
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0135125
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.40825.22744
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.31915178
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.106157
X-RAY DIFFRACTIONr_chiral_restr0.0570.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021060
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02173
X-RAY DIFFRACTIONr_nbd_refined0.2190.3240
X-RAY DIFFRACTIONr_nbd_other0.2020.3618
X-RAY DIFFRACTIONr_nbtor_refined0.1780.5466
X-RAY DIFFRACTIONr_nbtor_other0.0870.5480
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.5139
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.313
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3220.334
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.519
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9382629
X-RAY DIFFRACTIONr_mcbond_other0.2142250
X-RAY DIFFRACTIONr_mcangle_it1.4033952
X-RAY DIFFRACTIONr_scbond_it2.2334357
X-RAY DIFFRACTIONr_scangle_it3.36308
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 31 -
Rwork0.22 542 -
obs--89.25 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.578-3.6749-0.592827.18373.87241.71640.08210.13340.2824-0.86770.0936-0.9104-0.24250.0488-0.1757-0.0255-0.03820.05660.0440.0684-0.04397.81619.525.809
20.9988-1.52310.31214.28092.02410.6201-0.06560.02590.04490.39530.0514-0.2130.1218-0.00250.01420.02930.00730.0154-0.03470.0194-0.10585.6229.09714.795
311.13991.95395.06968.04340.86823.0653-0.26810.07261.28080.0186-0.1847-0.0336-0.48340.06520.45280.0024-0.0009-0.0211-0.02170.06770.06430.39941.08714.43
40.7085-0.7025-0.14310.54733.45992.13870.00110.0783-0.1339-0.1792-0.09710.29140.1477-0.05610.096-0.0299-0.0147-0.0042-0.0204-0.0006-0.0741-0.8289.1187.255
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 32
2X-RAY DIFFRACTION2A33 - 61
3X-RAY DIFFRACTION3A62 - 87
4X-RAY DIFFRACTION4A88 - 120

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