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

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Basic information

Entry
Database: PDB / ID: 6emj
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: 2.3 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
DepositionOct 2, 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 16, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,2685
Polymers96,2454
Non-polymers231
Water6,233346
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8660 Å2
ΔGint-60 kcal/mol
Surface area36810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.480, 73.869, 76.920
Angle α, β, γ (deg.)69.34, 78.05, 70.20
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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.67 Å3/Da / Density % sol: 53.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH 8.5 20 %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: Feb 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→45.79 Å / Num. obs: 44080 / % possible obs: 99.9 % / Redundancy: 8.2 % / Biso Wilson estimate: 54.42 Å2 / Rsym value: 0.168 / Net I/σ(I): 8
Reflection shellResolution: 2.3→2.38 Å / Rsym value: 0.947 / % possible all: 99.7

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Processing

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

Resolution: 2.3→45.79 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.936 / SU R Cruickshank DPI: 0.246 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.239 / SU Rfree Blow DPI: 0.188 / SU Rfree Cruickshank DPI: 0.192
RfactorNum. reflection% reflectionSelection details
Rfree0.211 2221 5.04 %RANDOM
Rwork0.165 ---
obs0.168 44079 100 %-
Displacement parametersBiso mean: 51.27 Å2
Baniso -1Baniso -2Baniso -3
1-5.2041 Å2-5.253 Å21.0117 Å2
2---3.2595 Å22.1539 Å2
3----1.9446 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: 1 / Resolution: 2.3→45.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6568 0 1 346 6915
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016734HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.179174HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2216SINUSOIDAL2
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_it6734HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.58
X-RAY DIFFRACTIONt_other_torsion17.77
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_contact7269SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2716 160 4.96 %
Rwork0.2147 3063 -
all0.2175 3223 -
obs--99.57 %
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)
12.01031.0089-0.39070.9576-0.26720.9749-0.0190.1958-0.1615-0.11960.039-0.0943-0.0318-0.0009-0.02-0.03430.07070.0043-0.0022-0.0186-0.0538-13.9445-17.8664-11.8367
21.6377-0.0420.11820.7648-0.06860.471-0.0257-0.08910.0488-0.03250.03060.1399-0.00440.0142-0.0049-0.0490.07040.0273-0.0458-0.0071-0.1167-28.2693-13.15-0.78
31.5088-1.40340.05611.54270.08340.9949-0.0738-0.2084-0.11050.10430.10140.1667-0.0524-0.0035-0.0277-0.081-0.03690.06250.0012-0.0111-0.0403-43.9497-3.898131.2444
41.8347-1.03730.21571.5497-0.14590.89-0.05760.0521-0.13490.02780.059-0.00690.00930.0826-0.0014-0.0729-0.00490.0536-0.0759-0.0382-0.0689-29.9467-6.61718.7961
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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