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- PDB-5hcg: CRYSTAL STRUCTURE OF FREE-CODV. -

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Basic information

Entry
Database: PDB / ID: 5hcg
TitleCRYSTAL STRUCTURE OF FREE-CODV.
Components
  • CODV heavy-chain
  • CODV light chain
KeywordsIMMUNE SYSTEM / cross-over dual variable immunoglobin / multifunctional biotherapeutic format / bispecific property / CODV
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsVallee, F. / Dupuy, A. / Rak, A.
CitationJournal: Mabs / Year: 2016
Title: CODV-Ig, a universal bispecific tetravalent and multifunctional immunoglobulin format for medical applications.
Authors: Steinmetz, A. / Vallee, F. / Beil, C. / Lange, C. / Baurin, N. / Beninga, J. / Capdevila, C. / Corvey, C. / Dupuy, A. / Ferrari, P. / Rak, A. / Wonerow, P. / Kruip, J. / Mikol, V. / Rao, E.
History
DepositionJan 4, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 1.2Jun 15, 2016Group: Database references
Revision 1.3Jan 10, 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 1.4Nov 20, 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
H: CODV heavy-chain
L: CODV light chain


Theoretical massNumber of molelcules
Total (without water)73,4482
Polymers73,4482
Non-polymers00
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-36 kcal/mol
Surface area30300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.920, 70.920, 272.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Antibody CODV heavy-chain


Mass: 37281.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody CODV light chain


Mass: 36166.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.34 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: HEPES 0,1M, PEG 2000 MME 17.5% / PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.68→49.3 Å / Num. obs: 20335 / % possible obs: 99.8 % / Redundancy: 12.7 % / Biso Wilson estimate: 74.32 Å2 / Net I/σ(I): 32.7
Reflection shellResolution: 2.68→2.83 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 4.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CODV part of 5FHX

5fhx


Resolution: 2.68→49.16 Å / Cor.coef. Fo:Fc: 0.9205 / Cor.coef. Fo:Fc free: 0.8646 / SU R Cruickshank DPI: 3.507 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.398 / SU Rfree Cruickshank DPI: 0.395
RfactorNum. reflection% reflectionSelection details
Rfree0.2965 1006 4.89 %RANDOM
Rwork0.2285 ---
obs0.2317 20563 99.96 %-
Displacement parametersBiso mean: 71.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.8033 Å20 Å20 Å2
2--3.8033 Å20 Å2
3----7.6067 Å2
Refine analyzeLuzzati coordinate error obs: 0.412 Å
Refinement stepCycle: LAST / Resolution: 2.68→49.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5015 0 0 87 5102
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015137HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.256992HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1690SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes112HARMONIC2
X-RAY DIFFRACTIONt_gen_planes749HARMONIC5
X-RAY DIFFRACTIONt_it5137HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.11
X-RAY DIFFRACTIONt_other_torsion21.59
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion684SEMIHARMONIC5
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_contact5581SEMIHARMONIC4
LS refinement shellResolution: 2.68→2.83 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3766 140 4.8 %
Rwork0.2708 2777 -
all0.2758 2917 -
obs--99.96 %

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