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- PDB-6ani: Coltuximab Fab in complex with anti-Kappa VHH domain -

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Basic information

Entry
Database: PDB / ID: 6ani
TitleColtuximab Fab in complex with anti-Kappa VHH domain
Components
  • Anti-Kappa VHH domain
  • Coltuximab Fab heavy chain
  • Coltuximab Fab light chain
KeywordsIMMUNE SYSTEM / Fab / antibody / CD19 / VHH domain
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesLama glama (llama)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsEreno Orbea, J. / Sicard, T. / Julien, J.-P.
CitationJournal: J. Mol. Biol. / Year: 2018
Title: Structural Basis of Enhanced Crystallizability Induced by a Molecular Chaperone for Antibody Antigen-Binding Fragments.
Authors: Ereno-Orbea, J. / Sicard, T. / Cui, H. / Carson, J. / Hermans, P. / Julien, J.P.
History
DepositionAug 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Oct 16, 2019Group: Advisory / Data collection / Structure summary / Category: database_PDB_caveat / pdbx_entry_details
Revision 1.3Nov 20, 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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Anti-Kappa VHH domain
K: Anti-Kappa VHH domain
H: Coltuximab Fab heavy chain
L: Coltuximab Fab light chain
I: Coltuximab Fab heavy chain
M: Coltuximab Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,5808
Polymers114,3966
Non-polymers1842
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10000 Å2
ΔGint-53 kcal/mol
Surface area49630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.390, 48.301, 128.547
Angle α, β, γ (deg.)90.00, 104.07, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Anti-Kappa VHH domain


Mass: 10315.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama)
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
#2: Antibody Coltuximab Fab heavy chain


Mass: 23840.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Coltuximab Fab light chain


Mass: 23041.549 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAnti-kappa VHH domain is represented as poly-UNK. The side chains were not included in the refinement.

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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: 2.47 Å3/Da / Density % sol: 50.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M magnesium chloride, 0.1 M HEPES, pH 7.0 and 14 % polyethyleneglycol (PEG) 3350 (w/v)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.4→46.596 Å / Num. obs: 43226 / % possible obs: 99.4 % / Redundancy: 4.33 % / Biso Wilson estimate: 36.53 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.074 / Net I/σ(I): 9.18
Reflection shellResolution: 2.4→2.44 Å / Rmerge(I) obs: 0.683 / Num. measured obs: 27663 / CC1/2: 0.583 / Rpim(I) all: 0.372

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementResolution: 2.4→46.6 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.286 2000 4.64 %
Rwork0.245 --
obs0.247 43095 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7651 0 12 162 7825
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037828
X-RAY DIFFRACTIONf_angle_d0.61810702
X-RAY DIFFRACTIONf_dihedral_angle_d10.1944674
X-RAY DIFFRACTIONf_chiral_restr0.0421241
X-RAY DIFFRACTIONf_plane_restr0.0041387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.39041390.3232862X-RAY DIFFRACTION100
2.46-2.52650.3681420.30572912X-RAY DIFFRACTION100
2.5265-2.60090.32211410.29382904X-RAY DIFFRACTION100
2.6009-2.68480.341440.2922955X-RAY DIFFRACTION100
2.6848-2.78070.32711400.28182868X-RAY DIFFRACTION100
2.7807-2.89210.32661420.28462906X-RAY DIFFRACTION100
2.8921-3.02370.35141420.27332941X-RAY DIFFRACTION100
3.0237-3.18310.3281420.25712911X-RAY DIFFRACTION100
3.1831-3.38240.28581430.2552936X-RAY DIFFRACTION100
3.3824-3.64350.29841430.2392941X-RAY DIFFRACTION100
3.6435-4.010.27471440.24082951X-RAY DIFFRACTION100
4.01-4.58980.2181430.20192943X-RAY DIFFRACTION100
4.5898-5.78090.24311450.20992973X-RAY DIFFRACTION100
5.7809-46.60450.26031500.22413092X-RAY DIFFRACTION100

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