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- PDB-5od8: Crystal structure of the RA-associated mAb B2 (Fab fragment) -

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Basic information

Entry
Database: PDB / ID: 5od8
TitleCrystal structure of the RA-associated mAb B2 (Fab fragment)
Components
  • B2 Fab fragment - Light chain
  • B2 Fab fragment - heavy chain
KeywordsIMMUNE SYSTEM / antibody Fab fragment / IMMUNE SYSTEM rheumatoid arthritis associated
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDobritzsch, D. / Ge, C. / Holmdahl, R. / Amara, K. / Malmstrom, V.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Knut and Alice Wallenberg FoundationKAW 2010.0148 Sweden
Swedish Research CouncilK2011-52X-07931-25-5 Sweden
CitationJournal: Arthritis Rheumatol / Year: 2019
Title: Structural Basis of Cross-Reactivity of Anti-Citrullinated Protein Antibodies.
Authors: Ge, C. / Xu, B. / Liang, B. / Lonnblom, E. / Lundstrom, S.L. / Zubarev, R.A. / Ayoglu, B. / Nilsson, P. / Skogh, T. / Kastbom, A. / Malmstrom, V. / Klareskog, L. / Toes, R.E.M. / Rispens, T. ...Authors: Ge, C. / Xu, B. / Liang, B. / Lonnblom, E. / Lundstrom, S.L. / Zubarev, R.A. / Ayoglu, B. / Nilsson, P. / Skogh, T. / Kastbom, A. / Malmstrom, V. / Klareskog, L. / Toes, R.E.M. / Rispens, T. / Dobritzsch, D. / Holmdahl, R.
History
DepositionJul 5, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: B2 Fab fragment - heavy chain
B: B2 Fab fragment - Light chain


Theoretical massNumber of molelcules
Total (without water)47,5122
Polymers47,5122
Non-polymers00
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-32 kcal/mol
Surface area19400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.410, 41.900, 97.490
Angle α, β, γ (deg.)90.00, 108.37, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-311-

HOH

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Components

#1: Antibody B2 Fab fragment - heavy chain


Mass: 24275.295 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: B cells
Cell line (production host): 293 embryonic kidney fibroblasts
Production host: Homo sapiens (human)
#2: Antibody B2 Fab fragment - Light chain


Mass: 23236.822 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: B cells
Cell line (production host): 293 embryonic kidney fibroblasts
Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.68 Å3/Da / Density % sol: 53.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% (w/v) PEG3350, 0.2 M Na3citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.2→92.53 Å / Num. obs: 25795 / % possible obs: 94.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 29.5 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.051 / Net I/σ(I): 10.8
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 3 / Num. unique obs: 1602 / CC1/2: 0.791 / Rpim(I) all: 0.243 / % possible all: 69.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ncj

3ncj


Resolution: 2.2→92.52 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.928 / SU B: 13.837 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.268 / ESU R Free: 0.211 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24254 1296 5 %RANDOM
Rwork0.19972 ---
obs0.20195 24454 94.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.519 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å21.33 Å2
2---0.75 Å2-0 Å2
3---0.11 Å2
Refinement stepCycle: 1 / Resolution: 2.2→92.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3335 0 0 218 3553
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.023419
X-RAY DIFFRACTIONr_bond_other_d0.0020.023062
X-RAY DIFFRACTIONr_angle_refined_deg1.3761.9434651
X-RAY DIFFRACTIONr_angle_other_deg0.90637156
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8345441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.78124.16125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.48615538
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1111512
X-RAY DIFFRACTIONr_chiral_restr0.0730.2529
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213782
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02678
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_it0.4851.4421770
X-RAY DIFFRACTIONr_mcbond_other0.4851.4421769
X-RAY DIFFRACTIONr_mcangle_it0.9042.162209
X-RAY DIFFRACTIONr_mcangle_other0.9042.1612210
X-RAY DIFFRACTIONr_scbond_it0.3431.4591649
X-RAY DIFFRACTIONr_scbond_other0.3431.4571647
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.652.172442
X-RAY DIFFRACTIONr_long_range_B_refined4.87817.5983600
X-RAY DIFFRACTIONr_long_range_B_other4.78916.8593544
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 56 -
Rwork0.283 1300 -
obs--68.04 %
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)
13.5739-1.3804-0.75912.13080.08351.03880.20780.31440.01850.061-0.2439-0.0434-0.02870.00140.03610.2362-0.0069-0.03580.265-0.00970.00982.005419.125614.3382
23.6326-0.7664-1.21091.31730.21530.7540.0067-0.2162-0.07660.4066-0.1239-0.1792-0.12910.32450.11720.381-0.0611-0.07560.33860.05460.07938.24612.531329.2407
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 230
2X-RAY DIFFRACTION2B1 - 213

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