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- PDB-3gje: Rational development of high-affinity T-cell receptor-like antibodies -

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Basic information

Entry
Database: PDB / ID: 3gje
TitleRational development of high-affinity T-cell receptor-like antibodies
Components
  • Fab Heavy Chain
  • Fab Light Chain
KeywordsIMMUNE SYSTEM / Antibody / pMHC / immune recognition
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsStewart-Jones, G. / Wadle, A. / Hombach, A. / Shenderov, E. / Held, G. / Fischer, E. / Kleber, S. / Stenner-Liewen, F. / Bauer, S. / McMichael, A. ...Stewart-Jones, G. / Wadle, A. / Hombach, A. / Shenderov, E. / Held, G. / Fischer, E. / Kleber, S. / Stenner-Liewen, F. / Bauer, S. / McMichael, A. / Knuth, A. / Abken, H. / Hombach, A.A. / Cerundolo, V. / Jones, E.Y. / Renner, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Rational development of high-affinity T-cell receptor-like antibodies
Authors: Stewart-Jones, G. / Wadle, A. / Hombach, A. / Shenderov, E. / Held, G. / Fischer, E. / Kleber, S. / Stenner-Liewen, F. / Bauer, S. / McMichael, A. / Knuth, A. / Abken, H. / Hombach, A.A. / ...Authors: Stewart-Jones, G. / Wadle, A. / Hombach, A. / Shenderov, E. / Held, G. / Fischer, E. / Kleber, S. / Stenner-Liewen, F. / Bauer, S. / McMichael, A. / Knuth, A. / Abken, H. / Hombach, A.A. / Cerundolo, V. / Jones, E.Y. / Renner, C.
History
DepositionMar 8, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Fab Light Chain
H: Fab Heavy Chain
A: Fab Light Chain
B: Fab Heavy Chain


Theoretical massNumber of molelcules
Total (without water)91,5804
Polymers91,5804
Non-polymers00
Water6,684371
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9280 Å2
ΔGint-57 kcal/mol
Surface area36430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.057, 117.057, 78.801
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Antibody Fab Light Chain


Mass: 22723.002 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHEN / Production host: Escherichia coli (E. coli) / Strain (production host): HB2151
#2: Antibody Fab Heavy Chain


Mass: 23066.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHEN / Production host: Escherichia coli (E. coli) / Strain (production host): HB2151
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.95 Å3/Da / Density % sol: 58.27 %
Crystal growMethod: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 5, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 44489 / Num. obs: 44489 / Observed criterion σ(F): 428360

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RZF

1rzf


Resolution: 2.3→25 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.894 / SU B: 8.471 / SU ML: 0.209 / Cross valid method: THROUGHOUT / ESU R: 0.329 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30231 2362 5 %RANDOM
Rwork0.22243 ---
obs0.22628 44459 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.399 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20 Å20 Å2
2--0.98 Å20 Å2
3----1.96 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6442 0 0 371 6813
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0226606
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0341.9539014
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.7735860
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.4324.5240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.614151010
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.3671520
X-RAY DIFFRACTIONr_chiral_restr0.1420.21016
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024990
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2460.22885
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.24317
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2423
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1741.54410
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.05426926
X-RAY DIFFRACTIONr_scbond_it2.73132604
X-RAY DIFFRACTIONr_scangle_it4.0294.52088
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.303→2.362 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 148 -
Rwork0.288 2931 -
obs--89.04 %

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