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- PDB-5vsh: CH1/Clambda Fab based on Pertuzumab -

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Basic information

Entry
Database: PDB / ID: 5vsh
TitleCH1/Clambda Fab based on Pertuzumab
Components
  • CH1/Clambda Fab heavy chain
  • CH1/Clambda Fab light chain
KeywordsIMMUNE SYSTEM / bispecific antibody / computational design / heavy chain/light chain interface / CH1/Ckappa interface / PertuzumAb
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å
AuthorsHendle, J.
CitationJournal: Protein Sci. / Year: 2017
Title: Computational design of a specific heavy chain/ kappa light chain interface for expressing fully IgG bispecific antibodies.
Authors: Froning, K.J. / Leaver-Fay, A. / Wu, X. / Phan, S. / Gao, L. / Huang, F. / Pustilnik, A. / Bacica, M. / Houlihan, K. / Chai, Q. / Fitchett, J.R. / Hendle, J. / Kuhlman, B. / Demarest, S.J.
History
DepositionMay 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 4, 2023Group: 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: CH1/Clambda Fab heavy chain
B: CH1/Clambda Fab light chain
C: CH1/Clambda Fab heavy chain
D: CH1/Clambda Fab light chain
E: CH1/Clambda Fab heavy chain
F: CH1/Clambda Fab light chain
H: CH1/Clambda Fab heavy chain
L: CH1/Clambda Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,59818
Polymers187,6378
Non-polymers96110
Water9,134507
1
A: CH1/Clambda Fab heavy chain
B: CH1/Clambda Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1985
Polymers46,9092
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-79 kcal/mol
Surface area18870 Å2
MethodPISA
2
C: CH1/Clambda Fab heavy chain
D: CH1/Clambda Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1014
Polymers46,9092
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-68 kcal/mol
Surface area18480 Å2
MethodPISA
3
E: CH1/Clambda Fab heavy chain
F: CH1/Clambda Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1014
Polymers46,9092
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-64 kcal/mol
Surface area18540 Å2
MethodPISA
4
H: CH1/Clambda Fab heavy chain
L: CH1/Clambda Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1985
Polymers46,9092
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-80 kcal/mol
Surface area18710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.531, 106.207, 156.772
Angle α, β, γ (deg.)90.000, 117.480, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-414-

HOH

21E-411-

HOH

31E-438-

HOH

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Components

#1: Antibody
CH1/Clambda Fab heavy chain


Mass: 23435.260 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody
CH1/Clambda Fab light chain


Mass: 23474.076 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 507 / 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: 2.71 Å3/Da / Density % sol: 54.56 %
Crystal growTemperature: 294 K / Method: vapor diffusion / Details: see publication

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 22, 2015
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.55→25.7 Å / Num. obs: 60826 / % possible obs: 93.1 % / Redundancy: 3.6 % / Biso Wilson estimate: 40.25 Å2 / Rmerge(I) obs: 0.138 / Net I/σ(I): 6.5
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 2 / Num. unique obs: 8443 / % possible all: 89.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
BUSTER2.11.5refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L7I

1l7i


Resolution: 2.55→25.7 Å / Cor.coef. Fo:Fc: 0.8485 / Cor.coef. Fo:Fc free: 0.7966 / SU R Cruickshank DPI: 0.737 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.705 / SU Rfree Blow DPI: 0.306 / SU Rfree Cruickshank DPI: 0.312
RfactorNum. reflection% reflectionSelection details
Rfree0.2552 3079 5.07 %RANDOM
Rwork0.2065 ---
obs0.209 60759 93.14 %-
Displacement parametersBiso max: 117.4 Å2 / Biso mean: 31.54 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--13.3744 Å20 Å2-13.9685 Å2
2--6.525 Å20 Å2
3---6.8495 Å2
Refine analyzeLuzzati coordinate error obs: 0.335 Å
Refinement stepCycle: final / Resolution: 2.55→25.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12762 0 50 507 13319
Biso mean--77.23 25.55 -
Num. residues----1702
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4219SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes251HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1987HARMONIC5
X-RAY DIFFRACTIONt_it13233HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1755SEMIHARMONIC5
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_contact14224SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d13233HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg18094HARMONIC21.04
X-RAY DIFFRACTIONt_omega_torsion2.73
X-RAY DIFFRACTIONt_other_torsion17.26
LS refinement shellResolution: 2.55→2.62 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2901 209 4.9 %
Rwork0.2358 4054 -
all0.2383 4263 -
obs--93.14 %

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