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- PDB-6and: Pinatuzumab Fab in complex with anti-Kappa VHH domain -

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Basic information

Entry
Database: PDB / ID: 6and
TitlePinatuzumab Fab in complex with anti-Kappa VHH domain
Components
  • Anti-kappa VHH domain
  • Pinatuzumab Fab Heavy chain
  • Pinatuzumab Fab light chain
KeywordsIMMUNE SYSTEM / Fab / antibody / CD22 / 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: 1.75 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 12, 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 1.2May 8, 2019Group: Advisory / Data collection / Structure summary / Category: database_PDB_caveat / pdbx_entry_details
Revision 1.3Nov 13, 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
K: Anti-kappa VHH domain
H: Pinatuzumab Fab Heavy chain
L: Pinatuzumab Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3044
Polymers58,2123
Non-polymers921
Water7,819434
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-30 kcal/mol
Surface area24850 Å2
Unit cell
Length a, b, c (Å)63.402, 72.947, 70.724
Angle α, β, γ (deg.)90.00, 110.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Anti-kappa VHH domain


Mass: 10315.707 Da / Num. of mol.: 1
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 Pinatuzumab Fab Heavy chain


Mass: 23833.525 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Pinatuzumab Fab light chain


Mass: 24062.736 Da / Num. of mol.: 1
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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / 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: 2.73 Å3/Da / Density % sol: 54.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M lithium sulfate, 0.1 M HEPES pH 7.4 and 25 % polyethyleneglycol (PEG) 3350

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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: Oct 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.75→46.142 Å / Num. obs: 57457 / % possible obs: 93.6 % / Redundancy: 3.35 % / Biso Wilson estimate: 18.14 Å2 / Net I/σ(I): 16.05
Reflection shell
Resolution (Å)Diffraction-ID
1.75-1.851
1.87-1.921

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XPREPdata reduction
PHENIXphasing
RefinementResolution: 1.75→46.012 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2899 2000 3.48 %
Rwork0.2407 --
obs0.2425 57457 94.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→46.012 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3853 0 6 434 4293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033940
X-RAY DIFFRACTIONf_angle_d0.695377
X-RAY DIFFRACTIONf_dihedral_angle_d15.5922337
X-RAY DIFFRACTIONf_chiral_restr0.044619
X-RAY DIFFRACTIONf_plane_restr0.004699
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.79380.3269980.2932716X-RAY DIFFRACTION65
1.7938-1.84230.33611110.27543094X-RAY DIFFRACTION75
1.8423-1.89650.2951300.26663582X-RAY DIFFRACTION85
1.8965-1.95770.35281470.25124087X-RAY DIFFRACTION98
1.9577-2.02770.30141510.24334180X-RAY DIFFRACTION100
2.0277-2.10890.29961500.23424174X-RAY DIFFRACTION100
2.1089-2.20480.30121520.22644195X-RAY DIFFRACTION100
2.2048-2.32110.2731500.2384166X-RAY DIFFRACTION100
2.3211-2.46650.27171500.24954178X-RAY DIFFRACTION100
2.4665-2.65690.31520.24784195X-RAY DIFFRACTION100
2.6569-2.92430.29441510.25274183X-RAY DIFFRACTION100
2.9243-3.34730.27181510.24284206X-RAY DIFFRACTION100
3.3473-4.21680.25621530.2254230X-RAY DIFFRACTION100
4.2168-46.02820.30871540.23394271X-RAY DIFFRACTION100

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