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

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Basic information

Entry
Database: PDB / ID: 6ell
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 1.2Nov 20, 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
Water7,800433
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 area3340 Å2
ΔGint-24 kcal/mol
Surface area19250 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 area3630 Å2
ΔGint-27 kcal/mol
Surface area19470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.984, 69.169, 77.667
Angle α, β, γ (deg.)117.11, 89.50, 103.39
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody fAB heavy chain


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


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.: 433 / 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: 2.58 Å3/Da / Density % sol: 52.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M TRIS, pH 7.5 25 %w/v PEG 6K

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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→44.4 Å / Num. obs: 71616 / % possible obs: 97.6 % / Redundancy: 3.43 % / Biso Wilson estimate: 37.86 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.068 / Net I/σ(I): 9.28
Reflection shellResolution: 1.9→2 Å / Rsym value: 0.72 / % 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

Resolution: 1.9→38 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.914 / SU R Cruickshank DPI: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.154 / SU Rfree Blow DPI: 0.145 / SU Rfree Cruickshank DPI: 0.147
RfactorNum. reflection% reflectionSelection details
Rfree0.245 3598 5.03 %RANDOM
Rwork0.203 ---
obs0.205 71499 97.4 %-
Displacement parametersBiso mean: 40.33 Å2
Baniso -1Baniso -2Baniso -3
1--1.7849 Å2-0.2999 Å2-1.6233 Å2
2--0.9632 Å2-0.7299 Å2
3---0.8217 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: 1 / Resolution: 1.9→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6565 0 0 433 6998
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016730HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.099168HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2215SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes147HARMONIC2
X-RAY DIFFRACTIONt_gen_planes977HARMONIC5
X-RAY DIFFRACTIONt_it6730HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.36
X-RAY DIFFRACTIONt_other_torsion17.01
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion888SEMIHARMONIC5
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_contact7171SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2669 259 5.06 %
Rwork0.2505 4864 -
all0.2513 5123 -
obs--94.19 %
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)
12.33481.3481-0.04471.18080.30440.4774-0.22620.23530.2766-0.13520.17260.19850.0171-0.00960.0536-0.06810.0291-0.0934-0.0553-0.007-0.041414.20525.2831-21.5527
20.97870.5677-0.17790.7813-0.30880.8518-0.0229-0.03050.06770.0096-0.02580.0242-0.07520.03950.0487-0.07320.0398-0.0383-0.0716-0.0191-0.065328.5068.9864-10.2276
32.0844-1.16560.8130.7991-0.16460.6988-0.09670.1250.23270.0602-0.0003-0.12-0.04660.0560.097-0.1103-0.0653-0.0002-0.0088-0.0193-0.050944.462922.863120.0957
40.9905-0.26460.10281.06990.21330.38810.0160.0720.0477-0.0877-0.02070.0757-0.0223-0.03010.0047-0.1112-0.02460.0021-0.0438-0.0297-0.070229.889816.8599.2734
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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