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- PDB-5odb: Crystal structure of the RA-associated mAb D10 (chimeric Fab fragment) -

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Basic information

Entry
Database: PDB / ID: 5odb
TitleCrystal structure of the RA-associated mAb D10 (chimeric Fab fragment)
Components
  • D10 Fab fragment - heavy chain
  • D10 Fab fragment - light 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: 1.53 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 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D10 Fab fragment - heavy chain
B: D10 Fab fragment - light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0214
Polymers46,8332
Non-polymers1882
Water8,071448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-39 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.368, 66.714, 72.764
Angle α, β, γ (deg.)90.00, 93.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody D10 Fab fragment - heavy chain


Mass: 23810.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: B cell clone of rheumatoid arthritis patient / Source: (gene. exp.) Homo sapiens (human) / Cell line: B cells / Production host: Homo sapiens (human)
#2: Antibody D10 Fab fragment - light chain


Mass: 23022.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: B cell clone of rheumatoid arthritis patient / Source: (gene. exp.) Homo sapiens (human) / Cell line: B cells / Production host: Homo sapiens (human)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 2.21 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.75
Details: 2.55 M ammonium sulfate, 0.1 M citrate pH 4.75, 0.1 M NDSB-256

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07201 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07201 Å / Relative weight: 1
ReflectionResolution: 1.53→47.26 Å / Num. obs: 67539 / % possible obs: 99.1 % / Redundancy: 2.8 % / Biso Wilson estimate: 13.2 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.037 / Net I/σ(I): 13.9
Reflection shellResolution: 1.53→1.56 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3360 / CC1/2: 0.721 / Rpim(I) all: 0.367 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2zuq, 2dag

2zuq

2dag


Resolution: 1.53→47.26 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.56 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.08 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21387 3408 5.1 %RANDOM
Rwork0.18752 ---
obs0.18885 64026 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.706 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å2-0 Å20.53 Å2
2---0.09 Å2-0 Å2
3---0.59 Å2
Refinement stepCycle: 1 / Resolution: 1.53→47.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3213 0 11 448 3672
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.023358
X-RAY DIFFRACTIONr_bond_other_d0.0020.023037
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.9464595
X-RAY DIFFRACTIONr_angle_other_deg0.92937052
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6495438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.20124.08125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.63815518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0321512
X-RAY DIFFRACTIONr_chiral_restr0.0880.2524
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213786
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02740
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_it1.2731.8161711
X-RAY DIFFRACTIONr_mcbond_other1.2741.8151710
X-RAY DIFFRACTIONr_mcangle_it2.1262.7182138
X-RAY DIFFRACTIONr_mcangle_other2.1252.722139
X-RAY DIFFRACTIONr_scbond_it1.5811.9791647
X-RAY DIFFRACTIONr_scbond_other1.5811.9791647
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5082.8952449
X-RAY DIFFRACTIONr_long_range_B_refined4.66322.4613685
X-RAY DIFFRACTIONr_long_range_B_other4.66522.4683686
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.53→1.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 250 -
Rwork0.254 4769 -
obs--99.5 %

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