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- PDB-3o6k: Crystal structure of anti-Tat HIV Fab'11H6H1 -

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Basic information

Entry
Database: PDB / ID: 3o6k
TitleCrystal structure of anti-Tat HIV Fab'11H6H1
Components
  • 11H6H1 Fab' heavy chain
  • 11H6H1 Fab' light chain
KeywordsIMMUNE SYSTEM / antigen-binding site / U-shaped groove / Tat HIV
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSerriere, J. / Gouet, P. / Guillon, C.
Citation
Journal: J.Mol.Biol. / Year: 2011
Title: Fab'-induced folding of antigenic N-terminal peptides from intrinsically disordered HIV-1 Tat revealed by X-ray crystallography.
Authors: Serriere, J. / Dugua, J.M. / Bossus, M. / Verrier, B. / Haser, R. / Gouet, P. / Guillon, C.
#1: Journal: Proteins / Year: 2010
Title: UV and X-ray structural studies of a 101-residue long Tat protein from a HIV-1 primary isolate and of its mutated, detoxified, vaccine candidate
Authors: Foucault, M. / Mayol, K. / Receveur-Brechot, V. / Bussat, M.C. / Klinguer-Hamour, C. / Verrier, B. / Beck, A. / Haser, R. / Gouet, P. / Guillon, C.
History
DepositionJul 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 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
L: 11H6H1 Fab' light chain
H: 11H6H1 Fab' heavy chain


Theoretical massNumber of molelcules
Total (without water)47,7722
Polymers47,7722
Non-polymers00
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-21 kcal/mol
Surface area19870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.143, 69.443, 62.456
Angle α, β, γ (deg.)90.00, 115.32, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody 11H6H1 Fab' light chain


Mass: 24219.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C
#2: Antibody 11H6H1 Fab' heavy chain


Mass: 23553.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 52.09 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.05M CaCl2, 0.1M Bis-Tris pH 6.5, 30% (v/v) polyethylene glycol 550 monomethyl ether , VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 2→59.13 Å / Num. obs: 32642 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 12.9
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 4.6 / Num. unique all: 4751 / % possible all: 99.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MLB

1mlb


Resolution: 2→36.93 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.952 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2465 1653 5.1 %RANDOM
Rwork0.1985 ---
all0.201 32642 --
obs0.201 30975 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.248 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0.01 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→36.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3326 0 0 125 3451
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0223412
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9991.9564649
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8745432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.97423.788132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.4415544
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2661516
X-RAY DIFFRACTIONr_chiral_restr0.1640.2522
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212566
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2381.52159
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.16723506
X-RAY DIFFRACTIONr_scbond_it3.4331253
X-RAY DIFFRACTIONr_scangle_it5.184.51143
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
Rfree0.255 113 -
Rwork0.22 2297 -
obs--99.63 %

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