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- PDB-6elj: FAB Fragment. AbVance: Increasing our knowledge of antibody struc... -

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Basic information

Entry
Database: PDB / ID: 6elj
TitleFAB Fragment. AbVance: Increasing our knowledge of antibody structural space to enable faster and better decision making in antibody drug discovery
Components
  • fAB heavy chain
  • fAB light chain
KeywordsIMMUNE SYSTEM / ANTIBODY / fAB FRAGMENT / AbVance project / Pistoia Alliance
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBenz, J. / Weigand, S. / Dengl, S. / Schlothauer, T. / Auer, J. / Ehler, A. / Kettenberger, H. / Lorenz, S. / Hirschheydt, T. / Georges, G.
CitationJournal: To Be Published
Title: AbVance: increasing our knowledge of antibody structural space to enable faster and better decision making in antibody drug discovery
Authors: Benz, J. / Georges, G.
History
DepositionSep 29, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: 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 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: fAB heavy chain
B: fAB light chain
H: fAB heavy chain
L: fAB light chain


Theoretical massNumber of molelcules
Total (without water)96,2454
Polymers96,2454
Non-polymers00
Water6,828379
1
A: fAB heavy chain
B: fAB light chain


Theoretical massNumber of molelcules
Total (without water)48,1232
Polymers48,1232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-28 kcal/mol
Surface area19100 Å2
MethodPISA
2
H: fAB heavy chain
L: fAB light chain


Theoretical massNumber of molelcules
Total (without water)48,1232
Polymers48,1232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-26 kcal/mol
Surface area19160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.578, 67.301, 76.615
Angle α, β, γ (deg.)116.76, 89.17, 105.07
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody fAB heavy chain / AbVance


Mass: 24570.447 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody fAB light chain / AbVance


Mass: 23552.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 2.37 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Na cacodylat 6.5 pH 25 %w/v PEG 4K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→44.24 Å / Num. obs: 67823 / % possible obs: 97.6 % / Redundancy: 3.42 % / Biso Wilson estimate: 31.03 Å2 / Rmerge(I) obs: 0.01 / Rsym value: 0.09 / Net I/σ(I): 7.55
Reflection shellResolution: 1.9→2 Å / Rsym value: 0.68 / % possible all: 96.2

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDSdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in house Fab structure

Resolution: 1.9→44.24 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / SU R Cruickshank DPI: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.143 / SU Rfree Blow DPI: 0.135 / SU Rfree Cruickshank DPI: 0.137
RfactorNum. reflection% reflectionSelection details
Rfree0.223 3426 5.05 %RANDOM
Rwork0.181 ---
obs0.184 67819 97.6 %-
Displacement parametersBiso mean: 35.97 Å2
Baniso -1Baniso -2Baniso -3
1--1.0866 Å20.1022 Å2-1.1203 Å2
2--0.7719 Å20.0113 Å2
3---0.3147 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: 1 / Resolution: 1.9→44.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6659 0 0 379 7038
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016830HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.119305HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2247SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes146HARMONIC2
X-RAY DIFFRACTIONt_gen_planes996HARMONIC5
X-RAY DIFFRACTIONt_it6830HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.82
X-RAY DIFFRACTIONt_other_torsion16.38
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion899SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7656SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 262 5.35 %
Rwork0.2269 4631 -
all0.2276 4893 -
obs--96.28 %
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)
11.31680.8844-0.10931.0979-0.15590.6688-0.03530.14440.041-0.07630.09980.07710.07810.0027-0.0645-0.04360.0262-0.0377-0.0425-0.0058-0.046713.42387.2182-19.6118
20.85120.513-0.04051.0355-0.48061.0920.03610.0159-0.0130.0217-0.05530.0028-0.06420.18350.0192-0.06720.0206-0.0156-0.0237-0.0168-0.080227.312811.3553-8.9401
31.0752-0.46130.48340.88660.01730.9153-0.0381-0.12160.13780.1093-0.0516-0.11710.04640.01070.0897-0.0901-0.0309-0.0047-0.0121-0.0349-0.043642.84525.052320.6796
41.1968-0.17280.490.8397-0.22240.6491-0.04070.02530.1259-0.03860.05360.0873-0.02360.0088-0.0129-0.0605-0.00870.0042-0.0538-0.0054-0.046228.829118.56629.8193
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ H|* }
4X-RAY DIFFRACTION4{ L|* }

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