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- PDB-6y1l: Crystal structure of the paraoxon-modified A.17 antibody FAB frag... -

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Basic information

Entry
Database: PDB / ID: 6y1l
TitleCrystal structure of the paraoxon-modified A.17 antibody FAB fragment - L47R mutant
Components
  • FAB A.17 L47R mutant HEAVY CHAIN
  • FAB A.17 L47R mutant Light CHAIN
KeywordsIMMUNE SYSTEM / QM/MM computation / designed biocatalysts / bioscavengers / phosphoryl transfer / organophosphorus agents
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / DIETHYL PHOSPHONATE
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsChatziefthimiou, S. / Mokrushina, Y. / Smirnov, I. / Gabibov, A. / Wilmanns, M.
Funding support Germany, Russian Federation, 2items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research05K14YEB Germany
Ministry of Education and Science of the Russian FederationRFMEFI60414X0069 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
DepositionFeb 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 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 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _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
H: FAB A.17 L47R mutant HEAVY CHAIN
L: FAB A.17 L47R mutant Light CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2124
Polymers54,0502
Non-polymers1622
Water8,791488
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-21 kcal/mol
Surface area19370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.723, 66.750, 66.220
Angle α, β, γ (deg.)90.000, 107.520, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody FAB A.17 L47R mutant HEAVY CHAIN


Mass: 27415.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Komagataella phaffii GS115 (fungus)
#2: Antibody FAB A.17 L47R mutant Light CHAIN


Mass: 26634.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Komagataella phaffii GS115 (fungus)
#3: Chemical ChemComp-DEP / DIETHYL PHOSPHONATE


Mass: 138.102 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H11O3P
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 488 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.38 Å3/Da / Density % sol: 48.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M ADA, pH 7.5 0.3M MgCl2 12% PEG 6K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.4→29.51 Å / Num. obs: 83469 / % possible obs: 96.9 % / Redundancy: 4.2 % / CC1/2: 0.999 / Net I/σ(I): 13.6
Reflection shellResolution: 1.4→1.42 Å / Num. unique obs: 15949 / CC1/2: 0.688

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Processing

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

2xza


Resolution: 1.4→29.507 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1999 4244 5.09 %
Rwork0.1707 79210 -
obs0.1722 83454 96.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.19 Å2 / Biso mean: 24.0372 Å2 / Biso min: 10.28 Å2
Refinement stepCycle: final / Resolution: 1.4→29.507 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3282 0 9 488 3779
Biso mean--25.22 36.79 -
Num. residues----440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123575
X-RAY DIFFRACTIONf_angle_d1.4374887
X-RAY DIFFRACTIONf_chiral_restr0.064554
X-RAY DIFFRACTIONf_plane_restr0.008635
X-RAY DIFFRACTIONf_dihedral_angle_d11.7671277
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4-1.41590.34171260.3071251491
1.4159-1.43260.31431290.2861253595
1.4326-1.450.33031460.2831256895
1.45-1.46840.27281270.2647265096
1.4684-1.48770.34541280.2629254595
1.4877-1.50810.27261460.2441264496
1.5081-1.52960.2611250.2357257196
1.5296-1.55250.28091350.2346265396
1.5525-1.57670.26011250.2175262797
1.5767-1.60260.22061420.2093256395
1.6026-1.63020.2841360.1984262996
1.6302-1.65990.21761480.1959261497
1.6599-1.69180.22521430.1853262497
1.6918-1.72630.21391620.1878258397
1.7263-1.76380.23341450.1716264797
1.7638-1.80490.1871540.1705265197
1.8049-1.850.21441400.1737264997
1.85-1.90.23111470.1713258896
1.9-1.95590.19541580.1696266498
1.9559-2.0190.17851520.1598265798
2.019-2.09120.2081330.1593266898
2.0912-2.17490.19081520.1631266198
2.1749-2.27380.2061520.1673269199
2.2738-2.39360.19971540.1705265197
2.3936-2.54350.21151410.1727270399
2.5435-2.73980.19841230.1717272699
2.7398-3.01530.18181430.1703270599
3.0153-3.4510.17481540.1574268198
3.451-4.34570.16791440.14012749100
4.3457-29.50.1721340.1498279999
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)
13.11970.45950.9332.07470.11883.08210.04910.1399-0.2397-0.1044-0.0956-0.0440.2734-0.0470.04450.1290.01530.01260.1305-0.00210.11780.1119-3.2086-1.5868
21.46150.2629-0.54171.8477-1.38962.29540.0482-0.08550.00070.1447-0.04490.06460.04520.0736-0.00820.1265-0.0251-0.01440.0814-0.00490.11310.4595-7.742928.45
32.58660.0517-0.54951.3701-0.22193.3990.12220.19210.18930.0203-0.00210.0783-0.18450.0366-0.10240.09020.00870.02360.10080.01410.1304-17.27965.07649.947
43.8130.01441.05960.6509-0.11991.4603-0.0746-0.15030.04780.08210.04270.0455-0.0232-0.11720.03430.11980.00670.00050.0922-0.01320.09738.26553.920937.6817
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain H and resid 1:117)H1 - 117
2X-RAY DIFFRACTION2(chain H and resid 118:224)H118 - 224
3X-RAY DIFFRACTION3(chain L and resid 2:107)L2 - 107
4X-RAY DIFFRACTION4(chain L and resid 108:219)L108 - 219

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