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- PDB-3lh2: Crystal structure of HIV epitope-scaffold 4E10_1VI7A_S0_002_N 4E1... -

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Basic information

Entry
Database: PDB / ID: 3lh2
TitleCrystal structure of HIV epitope-scaffold 4E10_1VI7A_S0_002_N 4E10 Fv complex
Components
  • 4E10_1VI7A_S0_002_N (T88)
  • Fv 4E10 heavy chain
  • Fv 4E10 light chain
KeywordsIMMUNE SYSTEM / EPITOPE-SCAFFOLD
Function / homologyAlpha-Beta Plaits - #240 / Alpha-Beta Plaits / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Function and homology information
Biological speciesARTIFICIAL GENE (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 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 21, 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
S: 4E10_1VI7A_S0_002_N (T88)
H: Fv 4E10 heavy chain
T: 4E10_1VI7A_S0_002_N (T88)
I: Fv 4E10 heavy chain
V: 4E10_1VI7A_S0_002_N (T88)
K: Fv 4E10 heavy chain
L: Fv 4E10 light chain
M: Fv 4E10 light chain
O: Fv 4E10 light chain
U: 4E10_1VI7A_S0_002_N (T88)
N: Fv 4E10 light chain
J: Fv 4E10 heavy chain


Theoretical massNumber of molelcules
Total (without water)141,89112
Polymers141,89112
Non-polymers00
Water2,378132
1
S: 4E10_1VI7A_S0_002_N (T88)
H: Fv 4E10 heavy chain
V: 4E10_1VI7A_S0_002_N (T88)
K: Fv 4E10 heavy chain
L: Fv 4E10 light chain
O: Fv 4E10 light chain


Theoretical massNumber of molelcules
Total (without water)70,9456
Polymers70,9456
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12980 Å2
ΔGint-97 kcal/mol
Surface area24820 Å2
MethodPISA
2
T: 4E10_1VI7A_S0_002_N (T88)
I: Fv 4E10 heavy chain
M: Fv 4E10 light chain
U: 4E10_1VI7A_S0_002_N (T88)
N: Fv 4E10 light chain
J: Fv 4E10 heavy chain


Theoretical massNumber of molelcules
Total (without water)70,9456
Polymers70,9456
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12880 Å2
ΔGint-97 kcal/mol
Surface area25100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.850, 145.950, 78.550
Angle α, β, γ (deg.)90.00, 92.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
4E10_1VI7A_S0_002_N (T88)


Mass: 8455.588 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The author states that 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: Antibody
Fv 4E10 heavy chain


Mass: 14712.454 Da / Num. of mol.: 4 / Mutation: W104A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL
#3: Antibody
Fv 4E10 light chain


Mass: 12304.698 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 3.06 Å3/Da / Density % sol: 59.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Na acetate, imidazole, pH 8, 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 SATURN 944+ / Detector: CCD / Date: Oct 22, 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: 2.65→28.01 Å / Num. all: 49017 / Num. obs: 49017 / % possible obs: 98.9 % / Redundancy: 3.88 % / Biso Wilson estimate: 62.3 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 9.4
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 3.68 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 2.7 / Num. unique all: 4883 / % possible all: 98.6

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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 Fv complex, with the Fv based on PDB ID 1TZG.

1tzg


Resolution: 2.65→26.7 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.878 / SU B: 11.214 / SU ML: 0.24 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.578 / ESU R Free: 0.325 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27023 2478 5.1 %RANDOM
Rwork0.22173 ---
obs0.22426 48955 98.53 %-
all-48955 --
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: 47.111 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.01 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.65→26.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8997 0 0 132 9129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0229217
X-RAY DIFFRACTIONr_bond_other_d0.0020.026082
X-RAY DIFFRACTIONr_angle_refined_deg0.9271.95312544
X-RAY DIFFRACTIONr_angle_other_deg0.6433.00214823
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1351202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.77623.782349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.617151408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7411547
X-RAY DIFFRACTIONr_chiral_restr0.0540.21436
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0210362
X-RAY DIFFRACTIONr_gen_planes_other00.021875
X-RAY DIFFRACTIONr_nbd_refined0.2080.31591
X-RAY DIFFRACTIONr_nbd_other0.2080.35906
X-RAY DIFFRACTIONr_nbtor_refined0.1880.54370
X-RAY DIFFRACTIONr_nbtor_other0.0890.55064
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.5512
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1010.56
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1320.323
X-RAY DIFFRACTIONr_symmetry_vdw_other0.230.349
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.58
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.58526112
X-RAY DIFFRACTIONr_mcbond_other0.06722488
X-RAY DIFFRACTIONr_mcangle_it1.05239526
X-RAY DIFFRACTIONr_scbond_it1.03943600
X-RAY DIFFRACTIONr_scangle_it1.69663014
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.647→2.715 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 161 -
Rwork0.295 3327 -
obs--95.09 %

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