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- PDB-2w65: Anti citrullinated Collagen type 2 antibody acc4 in complex with ... -

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Basic information

Entry
Database: PDB / ID: 2w65
TitleAnti citrullinated Collagen type 2 antibody acc4 in complex with a citrullinated peptide
Components
  • (ANTI-CITRULLINATED COLLAGEN TYPE II FAB ACC4) x 2
  • COLLAGEN DERIVED PEPTIDE PCII-CIT1
KeywordsIMMUNE SYSTEM / ARTHRITIS / COLLAGEN TYPE II / ANTIBODY ANTI-CITRULLIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsUysal, H. / Bockermann, R. / Nandakumar, K.S. / Sehnert, B. / Bajtner, E. / Engstrom, A. / Serre, G. / Burkhardt, H. / Thunnissen, M.M.G.M. / Holmdahl, R.
CitationJournal: J. Exp. Med. / Year: 2009
Title: Structure and pathogenicity of antibodies specific for citrullinated collagen type II in experimental arthritis.
Authors: Uysal, H. / Bockermann, R. / Nandakumar, K.S. / Sehnert, B. / Bajtner, E. / Engstrom, A. / Serre, G. / Burkhardt, H. / Thunnissen, M.M. / Holmdahl, R.
History
DepositionDec 17, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2017Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name / _diffrn_source.pdbx_synchrotron_site
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_validate_chiral / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_validate_chiral.auth_atom_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Dec 13, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ANTI-CITRULLINATED COLLAGEN TYPE II FAB ACC4
B: ANTI-CITRULLINATED COLLAGEN TYPE II FAB ACC4
C: ANTI-CITRULLINATED COLLAGEN TYPE II FAB ACC4
D: ANTI-CITRULLINATED COLLAGEN TYPE II FAB ACC4
E: COLLAGEN DERIVED PEPTIDE PCII-CIT1
F: COLLAGEN DERIVED PEPTIDE PCII-CIT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8068
Polymers96,6146
Non-polymers1922
Water3,783210
1
A: ANTI-CITRULLINATED COLLAGEN TYPE II FAB ACC4
B: ANTI-CITRULLINATED COLLAGEN TYPE II FAB ACC4
E: COLLAGEN DERIVED PEPTIDE PCII-CIT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4034
Polymers48,3073
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-41.8 kcal/mol
Surface area24440 Å2
MethodPQS
2
C: ANTI-CITRULLINATED COLLAGEN TYPE II FAB ACC4
D: ANTI-CITRULLINATED COLLAGEN TYPE II FAB ACC4
F: COLLAGEN DERIVED PEPTIDE PCII-CIT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4034
Polymers48,3073
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-36.7 kcal/mol
Surface area24570 Å2
MethodPQS
Unit cell
Length a, b, c (Å)57.200, 127.800, 71.900
Angle α, β, γ (deg.)90.00, 106.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.5697, -0.01805, -0.82166), (-0.01567, -0.99982, 0.0111), (-0.8217, 0.00655, -0.56988)5.34238, -29.13669, 10.63332
2given(0.59982, -0.03208, -0.79949), (-0.01117, -0.99943, 0.03173), (-0.80005, -0.0101, -0.59984)5.22112, -28.49842, 10.78115

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Components

#1: Antibody ANTI-CITRULLINATED COLLAGEN TYPE II FAB ACC4


Mass: 23480.402 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell line: MONOCLONAL B CELL HYBRIDOMA / Organ: SPLEEN / Strain: DBA/1
#2: Antibody ANTI-CITRULLINATED COLLAGEN TYPE II FAB ACC4


Mass: 23924.674 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell line: MONOCLONAL B CELL HYBRIDOMA / Organ: SPLEEN / Strain: DBA/1
#3: Protein/peptide COLLAGEN DERIVED PEPTIDE PCII-CIT1


Mass: 901.989 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: BASED ON THE C1 (359-367) EPITOPE OF COLLAGEN TYPE II WITH A CIRULLINE AT POSITION 360
Source: (synth.) MUS MUSCULUS (house mouse)
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O

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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: 2.71 Å3/Da / Density % sol: 54.64 % / Description: NONE
Crystal growDetails: 0.15 M AMMONIUM SULFATE, 20% PEG 3350 AND 10% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-5 / Wavelength: 0.907
DetectorType: MARRESEARCH / Detector: CCD / Details: MIRRORS
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.907 Å / Relative weight: 1
ReflectionResolution: 2.21→23.4 Å / Num. obs: 45714 / % possible obs: 96.6 % / Observed criterion σ(I): 3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.6
Reflection shellResolution: 2.21→2.31 Å / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4.4 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W60

2w60


Resolution: 2.21→24.23 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.894 / SU B: 12.63 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 0.325 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. LOOP 133-138 IS DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.285 2407 5 %RANDOM
Rwork0.234 ---
obs0.237 45714 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.01 Å2
Baniso -1Baniso -2Baniso -3
1-2.35 Å2-0 Å22.35 Å2
2---2.26 Å20 Å2
3---1.2 Å2
Refinement stepCycle: LAST / Resolution: 2.21→24.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6673 0 10 210 6893
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226851
X-RAY DIFFRACTIONr_bond_other_d0.0010.024563
X-RAY DIFFRACTIONr_angle_refined_deg1.841.9619341
X-RAY DIFFRACTIONr_angle_other_deg1.8763.00311179
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.0315865
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.58224.444252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.525151094
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.1171522
X-RAY DIFFRACTIONr_chiral_restr0.1050.21073
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027521
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021321
X-RAY DIFFRACTIONr_nbd_refined0.2010.21062
X-RAY DIFFRACTIONr_nbd_other0.2010.24227
X-RAY DIFFRACTIONr_nbtor_refined0.1750.23080
X-RAY DIFFRACTIONr_nbtor_other0.0910.23371
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2240
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2720.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2180.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6391.54494
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.02527065
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.38832792
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.0174.52276
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.21→2.27 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.332 166
Rwork0.239 3135

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