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- PDB-6ghg: Variable heavy - variable light domain and Fab-arm CrossMabs with... -

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Basic information

Entry
Database: PDB / ID: 6ghg
TitleVariable heavy - variable light domain and Fab-arm CrossMabs with charged residue exchanges
Components
  • Fab heavy chain
  • Fab light chain
KeywordsIMMUNE SYSTEM / ANTIBODY / FAB FRAGMENT / DP47 / ANG2 / VEGF / CROSSMAB / CHARGE VARIANTS
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsRegula, J. / Imhof-Jung, S. / Molhoj, M. / Benz, J. / Ehler, A. / Bujotzek, A. / Schaefer, W. / Klein, C.
CitationJournal: Protein Eng. Des. Sel. / Year: 2018
Title: Variable heavy-variable light domain and Fab-arm CrossMabs with charged residue exchanges to enforce correct light chain assembly.
Authors: Regula, J.T. / Imhof-Jung, S. / Molhoj, M. / Benz, J. / Ehler, A. / Bujotzek, A. / Schaefer, W. / Klein, C.
History
DepositionMay 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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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)93,01112
Polymers92,3094
Non-polymers7038
Water13,457747
1
A: Fab heavy chain
B: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5528
Polymers46,1542
Non-polymers3976
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-63 kcal/mol
Surface area19410 Å2
MethodPISA
2
H: Fab heavy chain
L: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4604
Polymers46,1542
Non-polymers3052
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-39 kcal/mol
Surface area19770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.560, 59.800, 79.090
Angle α, β, γ (deg.)99.49, 89.56, 92.61
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody Fab heavy chain


Mass: 22779.307 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: 23375.018 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.: 6 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 747 / 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: 3.01 Å3/Da / Density % sol: 59.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M MES, pH 6.5, 20% PEG2000MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99993 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99993 Å / Relative weight: 1
ReflectionResolution: 1.88→47.31 Å / Num. obs: 85296 / % possible obs: 97.5 % / Redundancy: 3.07 % / Biso Wilson estimate: 28.6 Å2 / Rsym value: 0.1 / Net I/σ(I): 7.01
Reflection shellResolution: 1.88→1.97 Å / Mean I/σ(I) obs: 1.05 / Rsym value: 0.7

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDSdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→18.95 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / SU R Cruickshank DPI: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.136 / SU Rfree Blow DPI: 0.126 / SU Rfree Cruickshank DPI: 0.125
RfactorNum. reflection% reflectionSelection details
Rfree0.226 4203 4.93 %RANDOM
Rwork0.195 ---
obs0.197 85182 97.5 %-
Displacement parametersBiso mean: 31.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.959 Å22.1031 Å2-1.2329 Å2
2---0.455 Å21.1388 Å2
3----0.5039 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 1.88→18.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6430 0 44 747 7221
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0096622HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.138990HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2206SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1102HARMONIC5
X-RAY DIFFRACTIONt_it6622HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.81
X-RAY DIFFRACTIONt_other_torsion16.17
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion863SEMIHARMONIC5
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_contact7692SEMIHARMONIC4
LS refinement shellResolution: 1.88→1.93 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2648 324 5.2 %
Rwork0.2463 5909 -
all0.2473 6233 -
obs--95.61 %
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)
10.1968-0.0304-0.03781.1776-0.61560.8380.02130.0202-0.01280.0197-0.03420.06280.02520.00230.0129-0.0096-0.0246-0.006-0.0278-0.005-0.0315-30.917710.2922-36.4297
20.2060.24730.02751.1154-0.18270.1723-0.0067-0.0259-0.0076-0.1130.0098-0.0560.0390.0391-0.00320.0121-0.00760.0107-0.0304-0.019-0.0108-24.0832.6763-51.407
31.216-0.09410.53220.14990.04630.7149-0.04870.0073-0.11710.04060.0220.0610.00160.00020.0267-0.0198-0.0290.0163-0.03650.0143-0.0106-45.869124.2104-21.9607
41.07170.37970.50250.06050.04020.19970.0071-0.1468-0.0420.0011-0.01780.0056-0.0435-0.09510.0107-0.0202-0.01810.02020.0184-0.0090.0022-53.349830.9113-6.237
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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