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- PDB-5tjd: Computer-based rational design of improved functionality for anti... -

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Basic information

Entry
Database: PDB / ID: 5tjd
TitleComputer-based rational design of improved functionality for antibody catalysts toward organophosphorus compounds
Components
  • FAB A.17 L47K mutant HEAVY CHAIN
  • FAB A.17 L47K mutant Light Chain
KeywordsIMMUNE SYSTEM / Antibody / rational design
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsChatziefthimiou, S. / Stepanova, A. / Smirnov, I. / Gabibov, A. / Wilmanns, M.
Funding support Germany, Russian Federation, 2items
OrganizationGrant numberCountry
BMBF05K14YEB Germany
RFMEFRFMEFI61614X0009 Russian Federation
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Multiscale computation delivers organophosphorus reactivity and stereoselectivity to immunoglobulin scavengers.
Authors: Mokrushina, Y.A. / Golovin, A.V. / Smirnov, I.V. / Chatziefthimiou, S.D. / Stepanova, A.V. / Bobik, T.V. / Zalevsky, A.O. / Zlobin, A.S. / Konovalov, K.A. / Terekhov, S.S. / Stepanov, A.V. / ...Authors: Mokrushina, Y.A. / Golovin, A.V. / Smirnov, I.V. / Chatziefthimiou, S.D. / Stepanova, A.V. / Bobik, T.V. / Zalevsky, A.O. / Zlobin, A.S. / Konovalov, K.A. / Terekhov, S.S. / Stepanov, A.V. / Pipiya, S.O. / Shamborant, O.G. / Round, E. / Belogurov Jr., A.A. / Bourenkov, G. / Makarov, A.A. / Wilmanns, M. / Xie, J. / Blackburn, G.M. / Gabibov, A.G. / Lerner, R.A.
History
DepositionOct 4, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 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 1.3Oct 16, 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: FAB A.17 L47K mutant HEAVY CHAIN
L: FAB A.17 L47K mutant Light Chain


Theoretical massNumber of molelcules
Total (without water)51,3702
Polymers51,3702
Non-polymers00
Water1,65792
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-24 kcal/mol
Surface area18850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.605, 66.637, 66.091
Angle α, β, γ (deg.)90.00, 107.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody FAB A.17 L47K mutant HEAVY CHAIN


Mass: 24763.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Komagataella pastoris GS115 (fungus)
#2: Antibody FAB A.17 L47K mutant Light Chain


Mass: 26606.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Komagataella pastoris GS115 (fungus)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.12 Å3/Da / Density % sol: 41.86 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M ADA pH 7.5 0.17 M MgCl2 20% (w/v) PEG-6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9673 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9673 Å / Relative weight: 1
ReflectionResolution: 2.1→49.35 Å / Num. obs: 24892 / % possible obs: 98.81 % / Redundancy: 4.7 % / Biso Wilson estimate: 39.43 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.08762 / Net I/σ(I): 10.43
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 4.8 % / Rmerge(I) obs: 1.07 / Mean I/σ(I) obs: 1.33 / CC1/2: 0.62 / % possible all: 97.07

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2xzc

2xzc


Resolution: 2.1→49.35 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 30.94
RfactorNum. reflection% reflection
Rfree0.2488 2457 5.12 %
Rwork0.1956 --
obs0.1984 24892 97.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→49.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3230 0 0 92 3322
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033310
X-RAY DIFFRACTIONf_angle_d0.7334504
X-RAY DIFFRACTIONf_dihedral_angle_d12.8931176
X-RAY DIFFRACTIONf_chiral_restr0.027514
X-RAY DIFFRACTIONf_plane_restr0.004574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.14050.34651510.27682454X-RAY DIFFRACTION94
2.1405-2.18410.44631310.27782498X-RAY DIFFRACTION97
2.1841-2.23160.29311380.282551X-RAY DIFFRACTION98
2.2316-2.28350.32841500.2612500X-RAY DIFFRACTION97
2.2835-2.34070.33281510.24872531X-RAY DIFFRACTION98
2.3407-2.40390.31961200.25242521X-RAY DIFFRACTION98
2.4039-2.47470.29391110.24492587X-RAY DIFFRACTION98
2.4747-2.55450.34841270.25442580X-RAY DIFFRACTION98
2.5545-2.64580.33381280.25362540X-RAY DIFFRACTION99
2.6458-2.75180.27971100.23372599X-RAY DIFFRACTION99
2.7518-2.8770.27871380.24462535X-RAY DIFFRACTION99
2.877-3.02870.26391460.22482517X-RAY DIFFRACTION97
3.0287-3.21840.27231070.20582541X-RAY DIFFRACTION98
3.2184-3.46680.21911670.18972501X-RAY DIFFRACTION98
3.4668-3.81560.20571630.16842481X-RAY DIFFRACTION98
3.8156-4.36740.22171450.1532552X-RAY DIFFRACTION98
4.3674-5.50130.23251400.152506X-RAY DIFFRACTION97
5.5013-49.36350.20111340.17742521X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4654-0.3728-0.03461.0374-0.69611.6276-0.02860.0963-0.0615-0.0541-0.09440.026-0.06520.0496-00.3184-0.0207-0.01030.3583-0.01250.3430.6902-2.9555-1.4342
20.77880.4638-0.11880.56890.36141.11810.07320.0001-0.12050.1593-0.0578-0.07730.12920.048500.3324-0.03-0.0020.2540.01490.31169.7741-8.199128.6312
31.5946-0.4715-1.31310.86810.34091.32550.00370.18820.07970.058-0.03710.0784-0.05460.024300.38110.00680.02750.4758-0.05830.4395-16.90584.789910.1561
40.9780.17350.14980.20960.41590.9186-0.0217-0.07710.03370.1535-0.0206-0.0463-0.0173-0.010500.3533-0.0162-0.01010.311-0.00060.33658.0114.313937.5617
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain H and resid 2:120)
2X-RAY DIFFRACTION2(chain H and resid 121:222)
3X-RAY DIFFRACTION3(chain L and resid 2:108)
4X-RAY DIFFRACTION4(chain L and resid 109:216)

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