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- PDB-7jkb: 2xVH Fab -

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Basic information

Entry
Database: PDB / ID: 7jkb
Title2xVH Fab
Components
  • Anti-Her2
  • Anti-lysozyme
KeywordsIMMUNE SYSTEM / antibody / 2xVH / Fab
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsLord, D.M. / Zhou, Y.F.
CitationJournal: Antibodies / Year: 2020
Title: Bringing the Heavy Chain to Light: Creating a Symmetric, Bivalent IgG-Like Bispecific.
Authors: Ramasubramanian, A. / Tennyson, R. / Magnay, M. / Kathuria, S. / Travaline, T. / Jain, A. / Lord, D.M. / Salemi, M. / Sullivan, C. / Magnay, T. / Hu, J. / Bric-Furlong, E. / Rival, P. / ...Authors: Ramasubramanian, A. / Tennyson, R. / Magnay, M. / Kathuria, S. / Travaline, T. / Jain, A. / Lord, D.M. / Salemi, M. / Sullivan, C. / Magnay, T. / Hu, J. / Bric-Furlong, E. / Rival, P. / Zhou, Y. / Hoffmann, D. / Brondyk, W. / Radosevic, K. / Chowdhury, P.S.
History
DepositionJul 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 3, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anti-lysozyme
B: Anti-Her2


Theoretical massNumber of molelcules
Total (without water)49,6982
Polymers49,6982
Non-polymers00
Water34219
1
A: Anti-lysozyme
B: Anti-Her2

A: Anti-lysozyme
B: Anti-Her2


Theoretical massNumber of molelcules
Total (without water)99,3974
Polymers99,3974
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area10780 Å2
ΔGint-56 kcal/mol
Surface area37520 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-23 kcal/mol
Surface area20180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.480, 195.000, 91.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-310-

HOH

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Components

#1: Antibody Anti-lysozyme


Mass: 24145.807 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Anti-Her2


Mass: 25552.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 3.16 Å3/Da / Density % sol: 61.11 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 1M lithium chloride, 0.1M citric acid pH 4.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.55→48.75 Å / Num. obs: 20965 / % possible obs: 99.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 18.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsDiffraction-ID% possible all
2.55-2.626.91.0442042199.9
11.4-48.755.20.028276198.6

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.14_3211refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: modeled Fab

Resolution: 2.55→48.75 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2916 2000 9.54 %
Rwork0.2541 18964 -
obs0.2578 20964 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 160.94 Å2 / Biso mean: 81.4778 Å2 / Biso min: 38.49 Å2
Refinement stepCycle: final / Resolution: 2.55→48.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3337 0 0 19 3356
Biso mean---67.37 -
Num. residues----449
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.5501-2.61380.37031400.34521336
2.6138-2.68450.40641390.35381313
2.6845-2.76350.39611420.34331343
2.7635-2.85270.36311390.33991323
2.8527-2.95460.41291440.35571357
2.9546-3.07290.44341410.33111333
3.0729-3.21270.37471420.33841351
3.2127-3.38210.34861410.29711334
3.3821-3.59390.35311410.28961346
3.5939-3.87130.35481430.28821359
3.8713-4.26060.28781430.2521354
4.2606-4.87670.21941440.19791369
4.8767-6.14220.2481470.21251391
6.14-48.750.21791540.20321455

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