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- PDB-3zl4: Antibody structural organization: Role of kappa - lambda chain co... -

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Basic information

Entry
Database: PDB / ID: 3zl4
TitleAntibody structural organization: Role of kappa - lambda chain constant domain switch in catalytic functionality
Components
  • A17 ANTIBODY FAB FRAGMENT HEAVY CHAIN
  • A17 ANTIBODY FAB FRAGMENT LAMBDA LIGHT CHAIN
KeywordsIMMUNE SYSTEM
Function / homology
Function and homology information


immunoglobulin complex / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Lambda-chain (AA -20 to 215) / IGH@ protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsChatziefthimiou, S.D. / Ponomarenko, N.A. / Kurkova, I.N. / Smirnov, A.V. / Smirnov, I.V. / Lamzin, V.S. / Gabibov, A.G. / Wilmanns, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Role of Kappa>Lambda Light-Chain Constant-Domain Switch in the Structure and Functionality of A17 Reactibody
Authors: Ponomarenko, N.A. / Chatziefthimiou, S.D. / Kurkova, I.N. / Mokrushina, Y.A. / Stepanova, A.V. / Smirnov, I.V. / Avakyan, E.M. / Bobik, T.V. / Mamedov, A. / Mitkevich, V.A. / Belogurov, A.J. ...Authors: Ponomarenko, N.A. / Chatziefthimiou, S.D. / Kurkova, I.N. / Mokrushina, Y.A. / Stepanova, A.V. / Smirnov, I.V. / Avakyan, E.M. / Bobik, T.V. / Mamedov, A. / Mitkevich, V.A. / Belogurov, A.J. / Fedorova, O.S. / Dubina, M. / Golovin, A. / Lamzin, V.S. / Friboulet, A. / Makarov, A.A. / Wilmanns, M. / Gabibov, A.G.
History
DepositionJan 28, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Mar 19, 2014Group: Database references
Revision 1.3Dec 17, 2014Group: Data collection
Revision 1.4Mar 7, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: A17 ANTIBODY FAB FRAGMENT HEAVY CHAIN
L: A17 ANTIBODY FAB FRAGMENT LAMBDA LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7263
Polymers53,5312
Non-polymers1951
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-19.6 kcal/mol
Surface area20810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.631, 60.631, 279.639
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Antibody A17 ANTIBODY FAB FRAGMENT HEAVY CHAIN


Mass: 27415.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PPICZALFA / Production host: KOMAGATAELLA PASTORIS GS115 (fungus) / References: UniProt: Q6GMX6*PLUS
#2: Antibody A17 ANTIBODY FAB FRAGMENT LAMBDA LIGHT CHAIN


Mass: 26115.768 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PPICZALFA / Production host: KOMAGATAELLA PASTORIS GS115 (fungus) / References: UniProt: A2NUT2*PLUS
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O

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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: 2.8 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal growpH: 6.5
Details: 0.1M MES PH 6.5, 0.25 M AMMONIUM SULFATE, 20% W/V PEG 5000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.2234
DetectorType: MARRESEARCH / Detector: CCD / Date: May 14, 2012
RadiationMonochromator: SI(III) CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2234 Å / Relative weight: 1
ReflectionResolution: 1.95→25 Å / Num. obs: 39334 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.6
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.1_1168)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XZA

2xza


Resolution: 1.95→24.399 Å / SU ML: 0.23 / σ(F): 1.38 / Phase error: 26.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2546 1971 5 %
Rwork0.2052 --
obs0.2077 39271 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.2 Å2
Refinement stepCycle: LAST / Resolution: 1.95→24.399 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3297 0 12 310 3619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073430
X-RAY DIFFRACTIONf_angle_d1.1184687
X-RAY DIFFRACTIONf_dihedral_angle_d14.6851216
X-RAY DIFFRACTIONf_chiral_restr0.074535
X-RAY DIFFRACTIONf_plane_restr0.006597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.99880.30881430.27782567X-RAY DIFFRACTION100
1.9988-2.05280.33071200.25712606X-RAY DIFFRACTION99
2.0528-2.11320.28371230.23872611X-RAY DIFFRACTION100
2.1132-2.18130.3061400.24082624X-RAY DIFFRACTION100
2.1813-2.25920.27921270.232640X-RAY DIFFRACTION100
2.2592-2.34960.31281550.22152576X-RAY DIFFRACTION100
2.3496-2.45650.27351280.21972654X-RAY DIFFRACTION100
2.4565-2.58580.27461410.22422626X-RAY DIFFRACTION100
2.5858-2.74770.30971470.2312660X-RAY DIFFRACTION100
2.7477-2.95950.27841380.23242660X-RAY DIFFRACTION100
2.9595-3.25670.25471550.21172670X-RAY DIFFRACTION100
3.2567-3.72650.28631420.19892717X-RAY DIFFRACTION100
3.7265-4.68950.18141610.16612756X-RAY DIFFRACTION100
4.6895-24.40070.21921510.17512933X-RAY DIFFRACTION100

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