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- PDB-5gks: Crystal structure of SLE patient-derived anti-DNA antibody -

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Basic information

Entry
Database: PDB / ID: 5gks
TitleCrystal structure of SLE patient-derived anti-DNA antibody
Components
  • IgG2, Fab (heavy chain)
  • lambda, Fab (light chain)
KeywordsIMMUNE SYSTEM / antibody / lupus / Fab
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / PHOSPHATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsArimori, T. / Sakakibara, S. / Kikutani, H. / Takagi, J.
CitationJournal: Sci Rep / Year: 2017
Title: Clonal evolution and antigen recognition of anti-nuclear antibodies in acute systemic lupus erythematosus
Authors: Sakakibara, S. / Arimori, T. / Yamashita, K. / Jinzai, H. / Motooka, D. / Nakamura, S. / Li, S. / Takeda, K. / Katayama, J. / El Hussien, M.A. / Narazaki, M. / Tanaka, T. / Standley, D.M. / ...Authors: Sakakibara, S. / Arimori, T. / Yamashita, K. / Jinzai, H. / Motooka, D. / Nakamura, S. / Li, S. / Takeda, K. / Katayama, J. / El Hussien, M.A. / Narazaki, M. / Tanaka, T. / Standley, D.M. / Takagi, J. / Kikutani, H.
History
DepositionJul 5, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IgG2, Fab (heavy chain)
B: lambda, Fab (light chain)
C: IgG2, Fab (heavy chain)
D: lambda, Fab (light chain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8816
Polymers92,6914
Non-polymers1902
Water3,495194
1
A: IgG2, Fab (heavy chain)
B: lambda, Fab (light chain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4413
Polymers46,3462
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-34 kcal/mol
Surface area18500 Å2
MethodPISA
2
C: IgG2, Fab (heavy chain)
D: lambda, Fab (light chain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4413
Polymers46,3462
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-32 kcal/mol
Surface area18530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.356, 41.167, 155.996
Angle α, β, γ (deg.)90.00, 113.07, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody IgG2, Fab (heavy chain)


Mass: 23397.178 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody lambda, Fab (light chain)


Mass: 22948.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.22 Å3/Da / Density % sol: 44.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG 8000, 0.1M Phosphate-citrate (pH 4.2), 0.2M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Aug 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 52059 / % possible obs: 99.9 % / Redundancy: 4.4 % / Rsym value: 0.083 / Net I/σ(I): 22.8
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.619 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GKR

5gkr


Resolution: 2.05→29.65 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / SU B: 11.658 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.236 / ESU R Free: 0.192 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25534 2618 5 %RANDOM
Rwork0.21745 ---
obs0.21935 49440 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 36.078 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å20 Å2-1.08 Å2
2---1.97 Å20 Å2
3---1.39 Å2
Refinement stepCycle: 1 / Resolution: 2.05→29.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6227 0 10 194 6431
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.026407
X-RAY DIFFRACTIONr_bond_other_d0.0020.025817
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.9498749
X-RAY DIFFRACTIONr_angle_other_deg0.904313493
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4625818
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.67324.044225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.05315969
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6811517
X-RAY DIFFRACTIONr_chiral_restr0.0850.2991
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217177
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021404
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_it0.2911.0043296
X-RAY DIFFRACTIONr_mcbond_other0.2911.0043295
X-RAY DIFFRACTIONr_mcangle_it0.531.5044106
X-RAY DIFFRACTIONr_mcangle_other0.531.5044107
X-RAY DIFFRACTIONr_scbond_it0.2281.0163111
X-RAY DIFFRACTIONr_scbond_other0.2061.013104
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.3711.5054632
X-RAY DIFFRACTIONr_long_range_B_refined3.9338.1916823
X-RAY DIFFRACTIONr_long_range_B_other3.9078.0566781
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.047→2.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 203 -
Rwork0.267 3559 -
obs--99 %
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)
14.65390.1065-0.95072.3086-0.18791.7883-0.0441-0.2656-0.03840.0475-0.07690.08870.00210.04910.12110.03120.01180.06570.29180.02480.1494-16.965-84.97842.617
23.4442-1.76530.97444.2041-2.76353.9245-0.0082-0.62780.04830.33110.05720.2058-0.1731-0.0967-0.0490.1443-0.06030.09770.5152-0.01930.0719-16.227-88.17363.806
34.21210.8102-0.46062.85090.13731.10930.01820.2139-0.1324-0.174-0.0458-0.04740.00680.00530.02760.04610.03110.0590.2883-0.02240.1159-13.478-105.59528.381
47.05713.41130.95635.63791.76754.153-0.01371.5234-0.2518-0.63650.2202-0.3911-0.36480.2749-0.20650.26390.1110.10680.7119-0.06920.0647-14.477-109.5887.456
53.8005-2.92740.20774.7214-1.10432.9228-0.4232-0.3139-0.09930.54640.29640.21910.34040.06510.12680.18690.04830.13020.30690.01530.156114.924-102.44546.171
64.1991.2301-3.52751.4451-1.19556.52740.3206-0.30410.17580.30480.09260.0421-0.4040.0872-0.41310.14840.02860.10060.2929-0.02420.114912.746-90.78157.522
72.2480.9409-0.31324.12211.28992.5442-0.1230.1708-0.0359-0.40880.010.06030.1430.03680.1130.12150.05170.06780.2927-0.01540.1154-45.398-123.48827.37
87.089-1.9379-2.96821.91092.02725.01010.39170.72220.1095-0.3476-0.06750.0099-0.2516-0.0292-0.32430.21190.0780.07860.37320.04120.1015-44.228-112.66314.062
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 116
2X-RAY DIFFRACTION2B2 - 110
3X-RAY DIFFRACTION3C2 - 116
4X-RAY DIFFRACTION4D2 - 110
5X-RAY DIFFRACTION5A117 - 212
6X-RAY DIFFRACTION6B111 - 209
7X-RAY DIFFRACTION7C117 - 213
8X-RAY DIFFRACTION8D111 - 209

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