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- PDB-5ado: Crystal structure of the paraoxon-modified A.17 antibody FAB frag... -

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Basic information

Entry
Database: PDB / ID: 5ado
TitleCrystal structure of the paraoxon-modified A.17 antibody FAB fragment - Light chain S35R mutant
Components(FAB A.17) x 2
KeywordsIMMUNE SYSTEM / ENZYME REPROGRAMMING / ANTIBODIES / IG SUPERFAMILY / IN SILICO ANTIBODY MATURATION
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / DIETHYL PHOSPHONATE
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsChatziefthimiou, S.D. / Smirnov, I.V. / Golovin, A.V. / Stepanova, A.V. / Peng, Y. / Zolotareva, O.I. / Belogurov, A.A. / Ponomarenko, N.A. / Blackburn, G.M. / Gabibov, A.A. ...Chatziefthimiou, S.D. / Smirnov, I.V. / Golovin, A.V. / Stepanova, A.V. / Peng, Y. / Zolotareva, O.I. / Belogurov, A.A. / Ponomarenko, N.A. / Blackburn, G.M. / Gabibov, A.A. / Lerner, R. / Wilmanns, M.
CitationJournal: Sci.Adv. / Year: 2016
Title: Robotic Qm/Mm-Driven Maturation of Antibody Combining Sites.
Authors: Smirnov, I.V. / Golovin, A.V. / Chatziefthimiou, S.D. / Stepanova, A.V. / Peng, Y. / Zolotareva, O.I. / Belogurov, A.A. / Kurkova, I.N. / Ponomarenko, N.A. / Wilmanns, M. / Blackburn, G.M. / ...Authors: Smirnov, I.V. / Golovin, A.V. / Chatziefthimiou, S.D. / Stepanova, A.V. / Peng, Y. / Zolotareva, O.I. / Belogurov, A.A. / Kurkova, I.N. / Ponomarenko, N.A. / Wilmanns, M. / Blackburn, G.M. / Gabibov, A.G. / Lerner, R.A.
History
DepositionAug 21, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 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 1.2Jan 10, 2024Group: 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_conn / 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_conn.pdbx_leaving_atom_flag / _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: FAB A.17
L: FAB A.17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2163
Polymers54,0782
Non-polymers1381
Water8,899494
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-13.2 kcal/mol
Surface area19090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.661, 67.075, 66.698
Angle α, β, γ (deg.)90.00, 107.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody FAB A.17


Mass: 27417.242 Da / Num. of mol.: 1 / Fragment: HEAVY CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PPICZALPHA JK1 / Production host: KOMAGATAELLA PASTORIS (fungus) / Strain (production host): GS115
#2: Antibody FAB A.17


Mass: 26660.377 Da / Num. of mol.: 1 / Fragment: LIGHT CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PPICZALPHA JK1 / Production host: KOMAGATAELLA PASTORIS (fungus) / Strain (production host): GS115
#3: Chemical ChemComp-DEP / DIETHYL PHOSPHONATE


Mass: 138.102 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H11O3P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 494 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsDIETHYL PHOSPHONATE (DEP): 1-ETHOXYPHOSPHONOYLOXYETHANE
Sequence detailsCHAIN L HAS MUTATION S35R

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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: 2.2 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 6.5
Details: 0.18 M MGCL2 16% (W/V) POLYETHYLENE GLYCOL 6000 0.1 M N-(2-ACETAMIDO) IMINODIACETIC ACID (ADA) PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.8266
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2012 / Details: MIRRORS
RadiationMonochromator: SI(III) CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8266 Å / Relative weight: 1
ReflectionResolution: 1.55→40 Å / Num. obs: 64020 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.5
Reflection shellResolution: 1.55→1.65 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 2 / % possible all: 99.8

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Processing

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

2xza


Resolution: 1.55→40 Å / SU ML: 0.19 / σ(F): 2 / Phase error: 21.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.199 3246 5.1 %
Rwork0.168 --
obs0.17 60774 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32 Å2
Refinement stepCycle: LAST / Resolution: 1.55→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3174 0 8 494 3676
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.01
X-RAY DIFFRACTIONf_angle_d1.2
X-RAY DIFFRACTIONf_dihedral_angle_d
X-RAY DIFFRACTIONf_chiral_restr
X-RAY DIFFRACTIONf_plane_restr
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.57320.36151400.28132554X-RAY DIFFRACTION100
1.5732-1.59770.31751470.25752662X-RAY DIFFRACTION100
1.5977-1.62390.25681210.24532623X-RAY DIFFRACTION100
1.6239-1.65190.26761360.23652640X-RAY DIFFRACTION100
1.6519-1.6820.28361500.22772634X-RAY DIFFRACTION100
1.682-1.71430.27111350.2222681X-RAY DIFFRACTION100
1.7143-1.74930.25611530.20992613X-RAY DIFFRACTION100
1.7493-1.78740.23691460.19922629X-RAY DIFFRACTION100
1.7874-1.82890.22841380.19592623X-RAY DIFFRACTION100
1.8289-1.87470.2341460.17782629X-RAY DIFFRACTION100
1.8747-1.92540.23291260.17642673X-RAY DIFFRACTION100
1.9254-1.9820.22121570.18522608X-RAY DIFFRACTION100
1.982-2.0460.21291400.17592659X-RAY DIFFRACTION100
2.046-2.11910.21441430.18472610X-RAY DIFFRACTION100
2.1191-2.20390.20071460.17492671X-RAY DIFFRACTION100
2.2039-2.30420.24431270.17942681X-RAY DIFFRACTION100
2.3042-2.42570.20481270.17662623X-RAY DIFFRACTION100
2.4257-2.57770.23891300.18262683X-RAY DIFFRACTION100
2.5777-2.77660.19211420.17892653X-RAY DIFFRACTION100
2.7766-3.0560.19621610.17312634X-RAY DIFFRACTION100
3.056-3.4980.18641620.1652631X-RAY DIFFRACTION100
3.498-4.40620.18531460.13382628X-RAY DIFFRACTION98
4.4062-40.21340.12971270.13572712X-RAY DIFFRACTION99
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)
14.047-0.22791.47052.7946-0.67964.7330.11240.6218-0.4155-0.3269-0.11290.09870.507-0.20450.02890.2345-0.0020.02370.362-0.07260.20851.0434-2.5708-2.6536
21.32810.01170.041.227-0.75322.19330.014-0.0086-0.08070.068-0.02150.07020.1368-0.05090.02680.1606-0.02350.00790.10150.00190.1748.7633-7.488524.4737
33.9316-0.035-2.1071.4757-0.25135.00840.12330.22750.1197-0.00820.04380.0834-0.1878-0.0538-0.15480.12920.02710.01960.1574-0.00040.1963-17.49074.573410.1825
46.13690.13531.29610.8264-0.07561.9008-0.0799-0.21350.06480.10550.04320.0749-0.0636-0.14970.02890.18430.00120.02010.11780.01060.15437.99354.41737.6108
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN H AND RESID 2:99)
2X-RAY DIFFRACTION2(CHAIN H AND RESID 100:222)
3X-RAY DIFFRACTION3(CHAIN L AND RESID 4:108)
4X-RAY DIFFRACTION4(CHAIN L AND RESID 109:216)

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