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- PDB-3lf6: Crystal structure of HIV epitope-scaffold 4E10_1XIZA_S0_001_N -

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Basic information

Entry
Database: PDB / ID: 3lf6
TitleCrystal structure of HIV epitope-scaffold 4E10_1XIZA_S0_001_N
ComponentsPutative phosphotransferase system
KeywordsIMMUNE SYSTEM / Epitope-scaffold
Function / homologyMannitol-specific EII; Chain A / Mannitol-specific EII; Chain A / 3-Layer(aba) Sandwich / Alpha Beta / PHOSPHATE ION
Function and homology information
Biological speciesARTIFICIAL GENE (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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 15, 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

Downloads & links

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Assembly

Deposited unit
A: Putative phosphotransferase system
B: Putative phosphotransferase system
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1795
Polymers36,8942
Non-polymers2853
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-34 kcal/mol
Surface area13120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.211, 81.975, 94.219
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative phosphotransferase system / 4E10_1XIZA_S0_001_N (T117) / mannitol/fructose-specific IIA domain containing protein


Mass: 18446.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The epitope-scaffold is based on domain IIA of the putative phosphotransferase system specific for mannitol/fructose from Salmonella typhimurium (PDB ID 1XIZ)
Source: (gene. exp.) ARTIFICIAL GENE (others) / Plasmid: PET29 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) STAR
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.58 Å3/Da / Density % sol: 52.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: DI-AMMONIUM PHOSPHATE, TRIS, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: Jan 3, 2008 / 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: 1.9→49.21 Å / Num. obs: 30053 / % possible obs: 97.5 % / Redundancy: 4.43 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 17.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2886 / % possible all: 95.2

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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 1XIZ

1xiz


Resolution: 1.9→31.5 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.918 / SU B: 11.788 / SU ML: 0.172 / Isotropic thermal model: Isotropic with 6 TLS groups / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27917 1420 5.1 %RANDOM
Rwork0.22324 ---
obs0.22615 26499 90.63 %-
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: 32.353 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å20 Å2
2--0.07 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.9→31.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2448 0 15 262 2725
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222577
X-RAY DIFFRACTIONr_bond_other_d0.0010.021679
X-RAY DIFFRACTIONr_angle_refined_deg1.0561.943532
X-RAY DIFFRACTIONr_angle_other_deg0.74334100
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1565323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.21124.173127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.84315403
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7791517
X-RAY DIFFRACTIONr_chiral_restr0.0610.2395
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022891
X-RAY DIFFRACTIONr_gen_planes_other00.02520
X-RAY DIFFRACTIONr_nbd_refined0.2050.3588
X-RAY DIFFRACTIONr_nbd_other0.2080.31918
X-RAY DIFFRACTIONr_nbtor_refined0.1860.51275
X-RAY DIFFRACTIONr_nbtor_other0.0870.51275
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2180.5360
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0530.38
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3540.310
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2660.513
X-RAY DIFFRACTIONr_mcbond_it0.76321618
X-RAY DIFFRACTIONr_mcbond_other0.1792623
X-RAY DIFFRACTIONr_mcangle_it1.17332586
X-RAY DIFFRACTIONr_scbond_it1.68641084
X-RAY DIFFRACTIONr_scangle_it2.3456939
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.501 80 -
Rwork0.494 1454 -
obs--68.33 %
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)
12.0572-0.19070.22111.68440.66942.4784-0.013-0.03530.13810.1742-0.09980.2013-0.0872-0.16080.11280.03880.01920.0167-0.067-0.0296-0.0881-11.556-11.42117.274
20.91970.0819-0.55341.8735-0.53642.15520.0327-0.0856-0.01460.0387-0.0663-0.0497-0.06230.19130.0336-0.0042-0.0061-0.0055-0.0527-0.0265-0.1206-1.073-11.13114.522
33.50560.20280.06085.1981-0.737711.29590.17290.02550.2730.0837-0.031-0.1269-0.65070.1335-0.14190.18-0.0313-0.0278-0.1684-0.074-0.1694-1.2-0.31925.829
42.5769-0.1127-0.08592.4744-0.01641.9073-0.02740.130.079-0.16310.0043-0.1436-0.22210.06470.0230.08410.0074-0.0013-0.05840.0346-0.170113.239-4.792-9.244
53.16790.5708-0.56922.4558-0.77951.49530.06450.00460.2063-0.0287-0.06340.1487-0.32710.0086-0.00110.07130.03610.0107-0.0530.0142-0.16256.682-0.857-0.865
64.30930.9836-1.18925.04320.4213.9162-0.0473-0.1622-0.07070.1662-0.0555-0.411-0.02210.3190.10280.0182-0.0406-0.0655-0.01930.0678-0.137621.98-5.0733.884
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 56
2X-RAY DIFFRACTION2A57 - 130
3X-RAY DIFFRACTION3A131 - 160
4X-RAY DIFFRACTION4B4 - 47
5X-RAY DIFFRACTION5B48 - 129
6X-RAY DIFFRACTION6B130 - 160

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