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- PDB-7rtp: Structure of full-length human lambda-6A light chain JTO in compl... -

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Basic information

Entry
Database: PDB / ID: 7rtp
TitleStructure of full-length human lambda-6A light chain JTO in complex with urea stabilizer 20 [1-(2-(7-(diethylamino)-4-methyl-2-oxo-2H-chromen-3-yl)ethyl)-3-(pyridin-3-ylmethyl)urea]
ComponentsJTO light chain
KeywordsIMMUNE SYSTEM / amyloidosis
Function / homologyChem-NY9 / PHOSPHATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsYan, N.L. / Wilson, I.A. / Kelly, J.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK46335 United States
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2022
Title: Amyloidogenic immunoglobulin light chain kinetic stabilizers comprising a simple urea linker module reveal a novel binding sub-site.
Authors: Yan, N.L. / Nair, R. / Chu, A. / Wilson, I.A. / Johnson, K.A. / Morgan, G.J. / Kelly, J.W.
History
DepositionAug 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: JTO light chain
B: JTO light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0225
Polymers46,4232
Non-polymers5983
Water6,431357
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-31 kcal/mol
Surface area20320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.643, 80.585, 94.645
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody JTO light chain


Mass: 23211.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-NY9 / N-{2-[7-(diethylamino)-4-methyl-2-oxo-2H-1-benzopyran-3-yl]ethyl}-N'-[(pyridin-3-yl)methyl]urea


Mass: 408.493 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H28N4O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.61 Å3/Da / Density % sol: 52.95 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350 and 0.25 M NH4H2PO4 at 23 degrees C

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.09→47.37 Å / Num. obs: 29655 / % possible obs: 99.8 % / Redundancy: 12.9 % / CC1/2: 1 / Rpim(I) all: 0.034 / Rsym value: 0.12 / Net I/σ(I): 14.9
Reflection shellResolution: 2.09→2.2 Å / Mean I/σ(I) obs: 3.7 / Num. unique obs: 4230 / CC1/2: 0.92 / Rpim(I) all: 0.21 / Rsym value: 0.72

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MG5

6mg5


Resolution: 2.09→47.37 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.921 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.199 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1484 5 %RANDOM
Rwork0.179 ---
obs0.1819 28112 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 156.13 Å2 / Biso mean: 30.592 Å2 / Biso min: 18.17 Å2
Baniso -1Baniso -2Baniso -3
1--1.51 Å20 Å2-0 Å2
2--2.07 Å20 Å2
3----0.56 Å2
Refinement stepCycle: final / Resolution: 2.09→47.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3260 0 40 357 3657
Biso mean--40.46 40.75 -
Num. residues----430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133410
X-RAY DIFFRACTIONr_bond_other_d0.0360.0172968
X-RAY DIFFRACTIONr_angle_refined_deg1.6781.6494665
X-RAY DIFFRACTIONr_angle_other_deg2.4391.5816966
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8065438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.19523.595153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.46315525
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8991514
X-RAY DIFFRACTIONr_chiral_restr0.0790.2461
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023956
X-RAY DIFFRACTIONr_gen_planes_other0.010.02662
LS refinement shellResolution: 2.09→2.141 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.27 104 -
Rwork0.244 2030 -
obs--97.93 %

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