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- PDB-4qt5: Crystal Structure of 3BD10: A Monoclonal Antibody against the TSH... -

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Basic information

Entry
Database: PDB / ID: 4qt5
TitleCrystal Structure of 3BD10: A Monoclonal Antibody against the TSH Receptor
Components
  • 3BD10 mouse monoclonal antibody, heavy chain
  • 3BD10 mouse monoclonal antibody, light chain
KeywordsIMMUNE SYSTEM / Graves disease / Antibody / TSH receptor / Thyroid
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHubbard, P.A. / Chen, C.R. / McLachlan, S.M. / Rapoport, B. / Murali, R.
CitationJournal: Mol.Endocrinol. / Year: 2015
Title: Crystal structure of a TSH receptor monoclonal antibody: insight into Graves' disease pathogenesis.
Authors: Chen, C.R. / Hubbard, P.A. / Salazar, L.M. / McLachlan, S.M. / Murali, R. / Rapoport, B.
History
DepositionJul 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: 3BD10 mouse monoclonal antibody, light chain
H: 3BD10 mouse monoclonal antibody, heavy chain
A: 3BD10 mouse monoclonal antibody, light chain
B: 3BD10 mouse monoclonal antibody, heavy chain


Theoretical massNumber of molelcules
Total (without water)93,4944
Polymers93,4944
Non-polymers00
Water1,892105
1
L: 3BD10 mouse monoclonal antibody, light chain
H: 3BD10 mouse monoclonal antibody, heavy chain


Theoretical massNumber of molelcules
Total (without water)46,7472
Polymers46,7472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-17 kcal/mol
Surface area19510 Å2
MethodPISA
2
A: 3BD10 mouse monoclonal antibody, light chain
B: 3BD10 mouse monoclonal antibody, heavy chain


Theoretical massNumber of molelcules
Total (without water)46,7472
Polymers46,7472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-19 kcal/mol
Surface area19630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.979, 136.979, 149.071
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11L
21A
12H
22B

NCS domain segments:

Component-ID: _ / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLULA1 - 2111 - 216
21GLUGLUAC1 - 2111 - 216
12GLNGLNHB1 - 2131 - 212
22GLNGLNBD1 - 2131 - 212

NCS ensembles :
ID
1
2

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Components

#1: Antibody 3BD10 mouse monoclonal antibody, light chain


Mass: 23768.404 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): SP2/0 / Production host: Mus musculus (house mouse)
#2: Antibody 3BD10 mouse monoclonal antibody, heavy chain


Mass: 22978.639 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): SP2/0 / Production host: Mus musculus (house mouse)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.4 Å3/Da / Density % sol: 48.78 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 7.4
Details: 20mM Tris.HCl, 11% PEG4K, pH 7.4, EVAPORATION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 7, 2013
RadiationMonochromator: Confocal Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→100.86 Å / Num. obs: 32117 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 8.9 % / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 7.6
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.626 / Mean I/σ(I) obs: 1.7 / Num. unique all: 32620 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4K23

4k23


Resolution: 2.5→100.86 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.889 / Cross valid method: THROUGHOUT / ESU R: 0.763 / ESU R Free: 0.33 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2785 1623 5.1 %RANDOM
Rwork0.23547 ---
all0.23766 30401 --
obs0.23766 30401 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.948 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å2-0 Å20 Å2
2---4.83 Å20 Å2
3---5.57 Å2
Refinement stepCycle: LAST / Resolution: 2.5→100.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6478 0 0 105 6583
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.026622
X-RAY DIFFRACTIONr_bond_other_d00.026094
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.9578996
X-RAY DIFFRACTIONr_angle_other_deg3.682314122
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5845820
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.18424.16250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.538151074
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5261528
X-RAY DIFFRACTIONr_chiral_restr0.0780.21034
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217288
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021420
X-RAY DIFFRACTIONr_mcbond_it2.3713.8253358
X-RAY DIFFRACTIONr_mcbond_other2.3713.8243357
X-RAY DIFFRACTIONr_mcangle_it3.8715.7274152
X-RAY DIFFRACTIONr_mcangle_other3.8715.7284153
X-RAY DIFFRACTIONr_scbond_it2.48243264
X-RAY DIFFRACTIONr_scbond_other2.4824.0023265
X-RAY DIFFRACTIONr_scangle_other4.0535.8934845
X-RAY DIFFRACTIONr_long_range_B_refined6.42829.7677026
X-RAY DIFFRACTIONr_long_range_B_other6.42429.7817020
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11L113610.16
12A113610.16
21H109560.13
22B109560.13
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 121 -
Rwork0.382 2224 -
obs-2345 99.74 %

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