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- PDB-2vl5: Structure of anti-collagen type II FAb CIIC1 -

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Basic information

Entry
Database: PDB / ID: 2vl5
TitleStructure of anti-collagen type II FAb CIIC1
Components(CIIC1 ANTICOLLAGEN FAB) x 2
KeywordsIMMUNE SYSTEM / RHEUMATOID FACTOR / ARTHRITIS / AUTOANTIBODIES / COLLAGEN TYPE II
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsUysal, H. / Sehnert, B. / Nandakumar, K.S. / Boiers, U. / Burkhardt, H. / Holmdahl, R. / Thunnissen, M.M.
CitationJournal: Mol.Immunol. / Year: 2008
Title: The Crystal Structure of the Pathogenic Collagen Type II-Specific Mouse Monoclonal Antibody Ciic1 Fab: Structure to Function Analysis.
Authors: Uysal, H. / Sehnert, B. / Nandakumar, K.S. / Boiers, U. / Burkhardt, H. / Holmdahl, R. / Thunnissen, M.M.
History
DepositionJan 8, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
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

Downloads & links

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Assembly

Deposited unit
A: CIIC1 ANTICOLLAGEN FAB
B: CIIC1 ANTICOLLAGEN FAB
C: CIIC1 ANTICOLLAGEN FAB
D: CIIC1 ANTICOLLAGEN FAB


Theoretical massNumber of molelcules
Total (without water)94,9444
Polymers94,9444
Non-polymers00
Water9,404522
1
A: CIIC1 ANTICOLLAGEN FAB
B: CIIC1 ANTICOLLAGEN FAB


Theoretical massNumber of molelcules
Total (without water)47,4722
Polymers47,4722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-34 kcal/mol
Surface area24610 Å2
MethodPQS
2
C: CIIC1 ANTICOLLAGEN FAB
D: CIIC1 ANTICOLLAGEN FAB


Theoretical massNumber of molelcules
Total (without water)47,4722
Polymers47,4722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-32 kcal/mol
Surface area24650 Å2
MethodPQS
Unit cell
Length a, b, c (Å)60.600, 78.000, 99.500
Angle α, β, γ (deg.)90.00, 83.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody CIIC1 ANTICOLLAGEN FAB


Mass: 23412.355 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell: MONOCLONAL B-CELL HYBRIDOMA / Cell line: MONOCLONAL B-CELL HYBRIDOMA / Organ: SPLEEN / Strain: DBA/1
#2: Antibody CIIC1 ANTICOLLAGEN FAB


Mass: 24059.471 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell: MONOCLONAL B-CELL HYBRIDOMA / Cell line: MONOCLONAL B-CELL HYBRIDOMA / Organ: SPLEEN / Strain: DBA/1
#3: 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: 2.54 Å3/Da / Density % sol: 51.56 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.2
Details: 0.2 SODIUM-FORMATE, 20 % PEG 3350, PH 7.2 HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97564
DetectorType: ADSC CCD / Detector: CCD / Details: MIRRORS
RadiationMonochromator: SI (111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97564 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. obs: 191077 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.66
Reflection shellResolution: 2.1→2.21 Å / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 4.04 / % possible all: 100

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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 1FSK
Resolution: 2.1→24.42 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.893 / SU B: 18.093 / SU ML: 0.239 / Cross valid method: THROUGHOUT / ESU R: 0.259 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.289 2659 5 %RANDOM
Rwork0.212 ---
obs0.216 50517 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å2-2.52 Å2
2---0.73 Å20 Å2
3---1.82 Å2
Refinement stepCycle: LAST / Resolution: 2.1→24.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6642 0 0 522 7164
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0226814
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6961.9519297
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2145865
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.71624.545264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.791151085
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7911525
X-RAY DIFFRACTIONr_chiral_restr0.1140.21048
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025135
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2190.22656
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.24395
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2432
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7651.54459
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.23727055
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9732769
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8734.52242
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: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.383 185
Rwork0.301 3516

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