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- PDB-6yxl: Crystal structure of ACPA F3 -

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Basic information

Entry
Database: PDB / ID: 6yxl
TitleCrystal structure of ACPA F3
Components
  • ACPA F3 Fab fragment - heavy chain
  • ACPA F3 Fab fragment - light chain
KeywordsIMMUNE SYSTEM / anti-citrullinated protein antibody Fab fragment
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGe, C. / Holmdahl, R.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: Sci Adv / Year: 2022
Title: Surface Ig variable domain glycosylation affects autoantigen binding and acts as threshold for human autoreactive B cell activation.
Authors: Kissel, T. / Ge, C. / Hafkenscheid, L. / Kwekkeboom, J.C. / Slot, L.M. / Cavallari, M. / He, Y. / van Schie, K.A. / Vergroesen, R.D. / Kampstra, A.S.B. / Reijm, S. / Stoeken-Rijsbergen, G. / ...Authors: Kissel, T. / Ge, C. / Hafkenscheid, L. / Kwekkeboom, J.C. / Slot, L.M. / Cavallari, M. / He, Y. / van Schie, K.A. / Vergroesen, R.D. / Kampstra, A.S.B. / Reijm, S. / Stoeken-Rijsbergen, G. / Koeleman, C. / Voortman, L.M. / Heitman, L.H. / Xu, B. / Pruijn, G.J.M. / Wuhrer, M. / Rispens, T. / Huizinga, T.W.J. / Scherer, H.U. / Reth, M. / Holmdahl, R. / Toes, R.E.M.
History
DepositionMay 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1May 25, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
HHH: ACPA F3 Fab fragment - heavy chain
LLL: ACPA F3 Fab fragment - light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2044
Polymers47,0152
Non-polymers1882
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-31 kcal/mol
Surface area19460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.886, 130.886, 61.026
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11HHH-461-

HOH

21HHH-489-

HOH

31HHH-498-

HOH

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Components

#1: Antibody ACPA F3 Fab fragment - heavy chain


Mass: 23570.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody ACPA F3 Fab fragment - light chain


Mass: 23445.096 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.78 Å3/Da / Density % sol: 55.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20mM Tris pH 7.4, 50mM NaCl, 0.2M Potassium thiocyanate, 2.2M Ammonium sulfate)

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Data collection

DiffractionMean temperature: 210 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9184 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.1→65.529 Å / Num. obs: 31556 / % possible obs: 100 % / Redundancy: 16.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.055 / Rrim(I) all: 0.164 / Net I/σ(I): 10.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.91-65.4413.30.0555010.9990.020.058
2.1-2.1616.81.46325240.8550.5221.554

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
REFMAC5.8.0258refinement
Aimless0.7.4data reduction
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ocx

5ocx


Resolution: 2.1→65.529 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 9.969 / SU ML: 0.131 / Cross valid method: FREE R-VALUE / ESU R: 0.197 / ESU R Free: 0.168
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2313 1551 4.924 %
Rwork0.1987 --
all0.2 --
obs-31497 99.978 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.449 Å2
Baniso -1Baniso -2Baniso -3
1--0.098 Å2-0 Å2-0 Å2
2---0.098 Å2-0 Å2
3---0.196 Å2
Refinement stepCycle: LAST / Resolution: 2.1→65.529 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3262 0 11 189 3462
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133345
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173018
X-RAY DIFFRACTIONr_angle_refined_deg1.7571.6514551
X-RAY DIFFRACTIONr_angle_other_deg1.3491.5727025
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3865419
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.1921.95159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.3215523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7411521
X-RAY DIFFRACTIONr_chiral_restr0.0720.2444
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023719
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02692
X-RAY DIFFRACTIONr_nbd_refined0.2530.2533
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.22861
X-RAY DIFFRACTIONr_nbtor_refined0.1650.21584
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21771
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2172
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0190.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.7370.213
X-RAY DIFFRACTIONr_nbd_other0.2830.235
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3120.26
X-RAY DIFFRACTIONr_mcbond_it1.6953.0531700
X-RAY DIFFRACTIONr_mcbond_other1.6943.051698
X-RAY DIFFRACTIONr_mcangle_it2.5164.5682111
X-RAY DIFFRACTIONr_mcangle_other2.5164.5682111
X-RAY DIFFRACTIONr_scbond_it2.3383.3441641
X-RAY DIFFRACTIONr_scbond_other2.3373.3451642
X-RAY DIFFRACTIONr_scangle_it3.7244.92435
X-RAY DIFFRACTIONr_scangle_other3.7234.9012436
X-RAY DIFFRACTIONr_lrange_it5.90435.9113522
X-RAY DIFFRACTIONr_lrange_other5.87635.7753507
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1550.2981360.2482144X-RAY DIFFRACTION100
2.155-2.2140.31120.2352124X-RAY DIFFRACTION100
2.214-2.2780.282980.2382053X-RAY DIFFRACTION100
2.278-2.3480.252930.2242038X-RAY DIFFRACTION100
2.348-2.4250.281940.2341946X-RAY DIFFRACTION100
2.425-2.510.2751080.2261868X-RAY DIFFRACTION100
2.51-2.6050.2521060.2021809X-RAY DIFFRACTION100
2.605-2.7110.3920.2071773X-RAY DIFFRACTION100
2.711-2.8310.264800.2071706X-RAY DIFFRACTION100
2.831-2.9690.265760.2031597X-RAY DIFFRACTION100
2.969-3.130.307660.2141582X-RAY DIFFRACTION100
3.13-3.320.245800.2081459X-RAY DIFFRACTION100
3.32-3.5490.22800.2091370X-RAY DIFFRACTION100
3.549-3.8330.239670.1911308X-RAY DIFFRACTION100
3.833-4.1980.195590.1661190X-RAY DIFFRACTION100
4.198-4.6930.134560.1381103X-RAY DIFFRACTION100
4.693-5.4180.132490.164970X-RAY DIFFRACTION100
5.418-6.6330.199470.238836X-RAY DIFFRACTION99.8869
6.633-9.3690.294420.209658X-RAY DIFFRACTION99.8573
9.369-65.5290.543100.222412X-RAY DIFFRACTION98.829
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)
11.736-1.582-0.43772.7411.04091.1043-0.1218-0.1640.08230.15980.08520.11160.06090.00170.03660.0229-0.0047-0.01150.0337-0.00280.0449-0.75225.369827.5061
21.2275-1.2672-0.60832.29591.2681.43460.03290.22710.158-0.0739-0.20520.1129-0.0741-0.13230.17220.03470.0232-0.02640.12810.02860.1131-11.068735.797616.186
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLHHH1 - 231
2X-RAY DIFFRACTION2ALLLLL1 - 213

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