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- PDB-6ztf: Crystal Structure of the anti-human P-Cadherin Fab CQY684 -

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Basic information

Entry
Database: PDB / ID: 6ztf
TitleCrystal Structure of the anti-human P-Cadherin Fab CQY684
Components
  • CQY684 Fab heavy-chain
  • CQY684 Fab light-chain
KeywordsIMMUNE SYSTEM / Immunoglobulin / Fab
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsRondeau, J.M. / Lehmann, S.
CitationJournal: Mol.Cancer Ther. / Year: 2021
Title: PCA062, a P-cadherin Targeting Antibody-Drug Conjugate, Displays Potent Antitumor Activity Against P-cadherin-expressing Malignancies.
Authors: Sheng, Q. / D'Alessio, J.A. / Menezes, D.L. / Karim, C. / Tang, Y. / Tam, A. / Clark, S. / Ying, C. / Connor, A. / Mansfield, K.G. / Rondeau, J.M. / Ghoddusi, M. / Geyer, F.C. / Gu, J. / ...Authors: Sheng, Q. / D'Alessio, J.A. / Menezes, D.L. / Karim, C. / Tang, Y. / Tam, A. / Clark, S. / Ying, C. / Connor, A. / Mansfield, K.G. / Rondeau, J.M. / Ghoddusi, M. / Geyer, F.C. / Gu, J. / McLaughlin, M.E. / Newcombe, R. / Elliot, G. / Tschantz, W.R. / Lehmann, S. / Fanton, C.P. / Miller, K. / Huber, T. / Rendahl, K.G. / Jeffry, U. / Pryer, N.K. / Lees, E. / Kwon, P. / Abraham, J.A. / Damiano, J.S. / Abrams, T.J.
History
DepositionJul 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 31, 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 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CQY684 Fab heavy-chain
B: CQY684 Fab light-chain
H: CQY684 Fab heavy-chain
L: CQY684 Fab light-chain


Theoretical massNumber of molelcules
Total (without water)99,3984
Polymers99,3984
Non-polymers00
Water13,818767
1
A: CQY684 Fab heavy-chain
B: CQY684 Fab light-chain


Theoretical massNumber of molelcules
Total (without water)49,6992
Polymers49,6992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-23 kcal/mol
Surface area20540 Å2
MethodPISA
2
H: CQY684 Fab heavy-chain
L: CQY684 Fab light-chain


Theoretical massNumber of molelcules
Total (without water)49,6992
Polymers49,6992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-21 kcal/mol
Surface area19920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.331, 109.384, 139.269
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody CQY684 Fab heavy-chain


Mass: 26420.283 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): TG1F-
#2: Antibody CQY684 Fab light-chain


Mass: 23278.812 Da / Num. of mol.: 2 / Fragment: Fab heavy-chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): TG1F-
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 767 / 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: 2.5 Å3/Da / Density % sol: 50.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.16M calcium acetate, 14.4% PEG 8,000, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99986 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 26, 2012 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99986 Å / Relative weight: 1
ReflectionResolution: 1.55→69.63 Å / Num. obs: 144981 / % possible obs: 100 % / Redundancy: 7.142 % / Biso Wilson estimate: 19.12 Å2 / Rmerge F obs: 0.066 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.06 / Χ2: 0.983 / Net I/σ(I): 20.56 / Num. measured all: 1035486 / Scaling rejects: 24
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.55-1.596.7660.4350.523.527185610621106200.563100
1.59-1.637.390.3250.4144.527652910358103560.445100
1.63-1.687.3440.2640.3465.397396910073100720.372100
1.68-1.737.2860.210.2766.6671080975797560.297100
1.73-1.797.1580.1640.2178.3667956949794940.234100
1.79-1.856.7650.1260.16610.4762310921192100.18100
1.85-1.927.120.0930.12614.0563259888988850.135100
1.92-27.4020.0670.09817.9563106852785260.106100
2-2.097.3530.0530.08121.1860372821482110.088100
2.09-2.197.2760.0450.0724.2757252787278690.076100
2.19-2.317.010.040.06226.452277745774570.067100
2.31-2.456.8170.0360.05728.3248593712971280.061100
2.45-2.627.5060.0290.0532.9650218669066900.054100
2.62-2.837.3990.0250.04436.6946043622362230.048100
2.83-3.17.220.0220.0440.141603576657620.04399.9
3.1-3.476.4380.020.03742.4633510520852050.0499.9
3.47-47.3280.0170.03548.3534055464746470.037100
4-4.97.2060.0150.03250.4528564396439640.034100
4.9-6.936.5080.0170.03246.3420175310631000.03499.8
6.93-69.637.0650.0140.03150.2612759181518060.03399.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å69.63 Å
Translation2.5 Å69.63 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASER1.3.1phasing
BUSTERrefinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L95

3l95


Resolution: 1.55→69.63 Å / Cor.coef. Fo:Fc: 0.9513 / Cor.coef. Fo:Fc free: 0.934 / SU R Cruickshank DPI: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.077 / SU Rfree Blow DPI: 0.075 / SU Rfree Cruickshank DPI: 0.073
RfactorNum. reflection% reflectionSelection details
Rfree0.207 7249 5 %RANDOM
Rwork0.188 ---
obs0.1889 144980 99.97 %-
Displacement parametersBiso max: 112.33 Å2 / Biso mean: 20.85 Å2 / Biso min: 8.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.7026 Å20 Å20 Å2
2---0.5035 Å20 Å2
3---1.2062 Å2
Refine analyzeLuzzati coordinate error obs: 0.171 Å
Refinement stepCycle: final / Resolution: 1.55→69.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6705 0 0 767 7472
Biso mean---28.06 -
Num. residues----879
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2293SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes154HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1004HARMONIC5
X-RAY DIFFRACTIONt_it6897HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion925SEMIHARMONIC5
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_contact8290SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6897HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg9404HARMONIC21.11
X-RAY DIFFRACTIONt_omega_torsion4.68
X-RAY DIFFRACTIONt_other_torsion13.63
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2313 530 5 %
Rwork0.2121 10078 -
all0.2131 10608 -
obs--99.97 %

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