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- PDB-5adp: Crystal structure of the A.17 antibody FAB fragment - Light chain... -

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Basic information

Entry
Database: PDB / ID: 5adp
TitleCrystal structure of the 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
Function and homology information
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 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 1.1Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
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
L: FAB A.17


Theoretical massNumber of molelcules
Total (without water)54,0782
Polymers54,0782
Non-polymers00
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-20.8 kcal/mol
Surface area19460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.547, 67.040, 66.950
Angle α, β, γ (deg.)90.00, 107.63, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 0.15 M MGCL2 18% (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: 10 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8123
DetectorType: MARRESEARCH MAR 165 / Detector: CCD / Date: Dec 8, 2011 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 2.13→19.42 Å / Num. obs: 24223 / % possible obs: 97.7 % / Observed criterion σ(I): 4.5 / Redundancy: 3.2 % / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.1
Reflection shellResolution: 2.13→2.2 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4.5 / % possible all: 92.2

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Processing

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

2xza


Resolution: 2.13→19.36 Å / SU ML: 0.24 / σ(F): 2 / Phase error: 23.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.22 2414 5.1 %
Rwork0.179 --
obs0.181 24208 97.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29 Å2
Refinement stepCycle: LAST / Resolution: 2.13→19.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3201 0 0 241 3442
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.8
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 (%)
2.1335-2.1770.27521460.23492395X-RAY DIFFRACTION89
2.177-2.22430.25411470.21312698X-RAY DIFFRACTION99
2.2243-2.27590.27251300.21312668X-RAY DIFFRACTION100
2.2759-2.33280.24711350.2192686X-RAY DIFFRACTION99
2.3328-2.39570.28691590.21682725X-RAY DIFFRACTION100
2.3957-2.46610.27461210.22052681X-RAY DIFFRACTION99
2.4661-2.54550.23561530.21542661X-RAY DIFFRACTION99
2.5455-2.63630.2651390.21122721X-RAY DIFFRACTION99
2.6363-2.74150.26441380.19922662X-RAY DIFFRACTION99
2.7415-2.86590.2441340.20482693X-RAY DIFFRACTION99
2.8659-3.01650.28281470.20282665X-RAY DIFFRACTION99
3.0165-3.20470.26711610.20332637X-RAY DIFFRACTION99
3.2047-3.45090.25221340.17722677X-RAY DIFFRACTION98
3.4509-3.79580.19941330.15832666X-RAY DIFFRACTION98
3.7958-4.33960.15761410.13722624X-RAY DIFFRACTION98
4.3396-5.44720.16331830.12612581X-RAY DIFFRACTION97
5.4472-19.36010.15271130.15672369X-RAY DIFFRACTION87
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)
12.99450.22230.3293.85670.45164.31430.0897-0.4198-0.33360.2954-0.1981-0.04270.37010.20620.06360.18660.00110.01730.2480.03490.199914.932-2.424134.5124
21.2506-0.0720.12691.39691.10962.6766-00.0298-0.1268-0.0315-0.08970.00340.1068-0.04960.08380.16150.0221-0.00370.1150.020.18437.0742-7.4946.7172
33.402-0.1646-1.01522.09340.43695.7820.1117-0.33190.07090.0759-0.0172-0.0454-0.2250.2436-0.08570.143-0.04970.0340.17060.01160.209534.15834.346521.0084
42.2890.15671.62650.2767-0.05432.1641-0.04450.19590.0851-0.05580.03380.0356-0.07770.0720.00750.18320.0154-0.00580.1191-0.00320.197710.30734.4916-2.4888
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN H AND RESID 2:98)
2X-RAY DIFFRACTION2(CHAIN H AND RESID 99:223)
3X-RAY DIFFRACTION3(CHAIN L AND RESID 2:92)
4X-RAY DIFFRACTION4(CHAIN L AND RESID 93:218)

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