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- PDB-2w60: Anti citrullinated Collagen type 2 antibody acc4 -

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Basic information

Entry
Database: PDB / ID: 2w60
TitleAnti citrullinated Collagen type 2 antibody acc4
Components(ANTI-CITRULLINATED COLLAGEN TYPE II FAB ACC4) x 2
KeywordsIMMUNE SYSTEM / ANTIBODY ANTI-CITRULLIN / ARTHRITIS
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / NITRATE ION
Function and homology information
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 16, 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 1.4Dec 13, 2023Group: 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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4113
Polymers47,3492
Non-polymers621
Water9,404522
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-29.9 kcal/mol
Surface area24260 Å2
MethodPQS
Unit cell
Length a, b, c (Å)44.800, 70.000, 136.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 23424.312 Da / Num. of mol.: 1 / 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.: 1 / 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: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 522 / 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: 2.38 Å3/Da / Density % sol: 48.35 % / Description: NONE
Crystal growpH: 8 / Details: 0.15 M AMMONIUM NITRATE, 25% PEG 3350, pH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.043
DetectorType: MARRESEARCH / Detector: CCD / Details: MIRRORS
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.043 Å / Relative weight: 1
ReflectionResolution: 1.45→68.2 Å / Num. obs: 64156 / % possible obs: 97.4 % / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.5
Reflection shellResolution: 1.45→1.55 Å / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 6.3 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0044refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VL5

2vl5


Resolution: 1.5→68.3 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.46 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22 3399 5 %RANDOM
Rwork0.169 ---
obs0.171 64528 97.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.77 Å2
Baniso -1Baniso -2Baniso -3
1--1.92 Å20 Å20 Å2
2--1.75 Å2-0 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.5→68.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3321 0 4 522 3847
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223493
X-RAY DIFFRACTIONr_bond_other_d0.0040.022308
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.9544786
X-RAY DIFFRACTIONr_angle_other_deg1.4973.0045683
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5945456
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.53824.688128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.26515564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9411510
X-RAY DIFFRACTIONr_chiral_restr0.1180.2552
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213900
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02672
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2451.52229
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.74823640
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.61431264
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.4614.51141
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: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.243 235
Rwork0.189 4729
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)
10.45660.2273-0.28950.6331-0.08170.4778-0.00290.04350.0364-0.08080.03040.03210.0116-0.0401-0.02750.18370.0033-0.00260.04440.00260.0937-17.1769-9.2394-17.5258
20.238-0.0326-0.10530.02870.05450.6981-0.0106-0.00590.01180.0743-0.00130.01260.0892-0.02510.01190.2406-0.0090.00320.0360.00450.093-26.8849-3.935117.3791
30.35880.05020.12260.89420.15420.41280.0155-0.00060.0318-0.05840.0088-0.0393-0.0965-0.0145-0.02420.1984-0.00350.01480.04460.00230.0951-22.48742.795714.9541
41.33240.65711.42781.75041.67012.28450.0445-0.23670.1362-0.1965-0.155-0.0207-0.2295-0.36230.11040.28540.0749-0.00150.1188-0.02940.1003-30.28947.037119.4172
50.25650.4001-0.19681.0009-0.26290.43290.0216-0.01120.00260.0172-0.02750.0025-0.05530.02210.0060.18480.0010.00060.04180.0030.09421.55621.3384-11.5146
61.32860.8249-0.78530.6745-0.43140.87570.0298-0.14570.0512-0.0094-0.02040.01230.05410.0977-0.00940.2401-0.01030.00150.0555-0.00880.0846-12.541-1.532420.9406
712.85234.93553.0162.48560.75460.9937-0.05060.4196-0.7752-0.32580.1013-0.40390.2110.1642-0.05070.36540.09880.15480.09920.0650.3158-10.6676-16.586225.2192
81.08460.8262-0.84790.6766-0.57760.95040.0577-0.131-0.03480.0173-0.0681-0.00570.04990.130.01040.2222-0.004-0.00650.06380.0060.0886-12.3283-4.643822.7718
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 115
2X-RAY DIFFRACTION2A116 - 136
3X-RAY DIFFRACTION3A137 - 190
4X-RAY DIFFRACTION4A191 - 218
5X-RAY DIFFRACTION5B1 - 109
6X-RAY DIFFRACTION6B110 - 156
7X-RAY DIFFRACTION7B157 - 162
8X-RAY DIFFRACTION8B163 - 217

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