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- PDB-5fcs: Diabody -

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Basic information

Entry
Database: PDB / ID: 5fcs
TitleDiabody
Components(Diabody) x 2
KeywordsIMMUNE SYSTEM / antibody / diabody / Pcad / CD3
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.01 Å
AuthorsMosyak, L. / Root, A.
CitationJournal: Antibodies / Year: 2016
Title: Development of PF-06671008, a Highly Potent Anti-P-cadherin/Anti-CD3 Bispecific DART Molecule with Extended Half-Life for the Treatment of Cancer.
Authors: Root, A.R. / Cao, W. / Li, B. / LaPan, P. / Meade, C. / Sanford, J. / Jin, M. / O'Sullivan, C. / Cummins, E. / Lambert, M. / Sheehan, A.D. / Ma, W. / Gatto, S. / Kerns, K. / Lam, K. / ...Authors: Root, A.R. / Cao, W. / Li, B. / LaPan, P. / Meade, C. / Sanford, J. / Jin, M. / O'Sullivan, C. / Cummins, E. / Lambert, M. / Sheehan, A.D. / Ma, W. / Gatto, S. / Kerns, K. / Lam, K. / D'Antona, A.M. / Zhu, L. / Brady, W.A. / Benard, S. / King, A. / He, T. / Racie, L. / Arai, M. / Barrett, D. / Stochaj, W. / LaVallie, E.R. / Apgar, J.R. / Svenson, K. / Mosyak, L. / Yang, Y. / Chichili, G.R. / Liu, L. / Li, H. / Burke, S. / Johnson, S. / Alderson, R. / Finlay, W.J.J. / Lin, L. / Olland, S. / Somers, W. / Bonvini, E. / Gerber, H.P. / May, C. / Moore, P.A. / Tchistiakova, L. / Bloom, L.
History
DepositionDec 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
H: Diabody
L: Diabody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5457
Polymers53,0652
Non-polymers4805
Water10,178565
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-104 kcal/mol
Surface area19200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.811, 142.811, 62.685
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Antibody Diabody


Mass: 25871.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Diabody


Mass: 27192.873 Da / Num. of mol.: 1
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


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 565 / 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: 3.48 Å3/Da / Density % sol: 64.63 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: 0.5M LiSO4 PEG 8000K 15%

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Data collection

DiffractionMean temperature: 270 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.01→29.43 Å / Num. obs: 47372 / % possible obs: 91 % / Redundancy: 9.2 % / Biso Wilson estimate: 30.53 Å2 / Net I/σ(I): 2.4

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Processing

Software
NameVersionClassification
BUSTER2.11.1refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.01→29.43 Å / Cor.coef. Fo:Fc: 0.9485 / Cor.coef. Fo:Fc free: 0.9266 / SU R Cruickshank DPI: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.142 / SU Rfree Blow DPI: 0.128 / SU Rfree Cruickshank DPI: 0.123
RfactorNum. reflection% reflectionSelection details
Rfree0.2048 2374 5.01 %RANDOM
Rwork0.176 ---
obs0.1775 47372 96.5 %-
Displacement parametersBiso mean: 32.41 Å2
Baniso -1Baniso -2Baniso -3
1-1.7243 Å20 Å20 Å2
2--1.7243 Å20 Å2
3----3.4485 Å2
Refine analyzeLuzzati coordinate error obs: 0.207 Å
Refinement stepCycle: 1 / Resolution: 2.01→29.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3529 0 25 572 4126
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013628HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.084938HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1168SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes72HARMONIC2
X-RAY DIFFRACTIONt_gen_planes538HARMONIC5
X-RAY DIFFRACTIONt_it3628HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.76
X-RAY DIFFRACTIONt_other_torsion14.39
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion471SEMIHARMONIC5
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_contact4273SEMIHARMONIC4
LS refinement shellResolution: 2.01→2.06 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2522 166 5.02 %
Rwork0.2156 3138 -
all0.2174 3304 -
obs--96.5 %

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