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- PDB-8fo3: Structure of full-length amyloidogenic immunoglobulin light chain... -

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Basic information

Entry
Database: PDB / ID: 8fo3
TitleStructure of full-length amyloidogenic immunoglobulin light chain H9 in complex with (E)-3-nitro-4-(2-(2-phenylpropylidene)hydrazineyl)benzenesulfonamide
ComponentsH9 immunoglobulin light chain
KeywordsIMMUNE SYSTEM / light chain / amyloidosis / stabilizer
Function / homologyPHOSPHATE ION / Chem-Y4K
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYan, N.L. / Wilson, I.A. / Kelly, J.W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL157566 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL154732 United States
CitationJournal: Isr.J.Chem. / Year: 2023
Title: Crystal Structures of Diaryl Hydrazone and Sulfone Stabilizers in Complex with an Amyloidogenic Light Chain Reveal an Alternate Ligand-Binding Cavity
Authors: Yan, N.L. / Wilson, I.A. / Kelly, J.W.
History
DepositionDec 29, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H9 immunoglobulin light chain
B: H9 immunoglobulin light chain
C: H9 immunoglobulin light chain
D: H9 immunoglobulin light chain
G: H9 immunoglobulin light chain
H: H9 immunoglobulin light chain
I: H9 immunoglobulin light chain
J: H9 immunoglobulin light chain
E: H9 immunoglobulin light chain
F: H9 immunoglobulin light chain
K: H9 immunoglobulin light chain
L: H9 immunoglobulin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)273,26824
Polymers270,59612
Non-polymers2,67212
Water25,0411390
1
A: H9 immunoglobulin light chain
B: H9 immunoglobulin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6405
Polymers45,0992
Non-polymers5403
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-24 kcal/mol
Surface area19620 Å2
MethodPISA
2
C: H9 immunoglobulin light chain
D: H9 immunoglobulin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4503
Polymers45,0992
Non-polymers3501
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-25 kcal/mol
Surface area19730 Å2
MethodPISA
3
G: H9 immunoglobulin light chain
H: H9 immunoglobulin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6405
Polymers45,0992
Non-polymers5403
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-21 kcal/mol
Surface area19160 Å2
MethodPISA
4
I: H9 immunoglobulin light chain
J: H9 immunoglobulin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4503
Polymers45,0992
Non-polymers3501
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-21 kcal/mol
Surface area19510 Å2
MethodPISA
5
E: H9 immunoglobulin light chain
F: H9 immunoglobulin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5454
Polymers45,0992
Non-polymers4452
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-21 kcal/mol
Surface area19220 Å2
MethodPISA
6
K: H9 immunoglobulin light chain
L: H9 immunoglobulin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5454
Polymers45,0992
Non-polymers4452
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-22 kcal/mol
Surface area19590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.141, 95.655, 125.918
Angle α, β, γ (deg.)106.31, 92.93, 90.16
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody
H9 immunoglobulin light chain


Mass: 22549.658 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-Y4K / 3-nitro-4-{2-[(2S)-2-phenylpropyl]hydrazinyl}benzene-1-sulfonamide


Mass: 350.393 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C15H18N4O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1390 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.69 Å3/Da / Density % sol: 54.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 20% PEG3350, 0.2 M potassium phosphate monobasic, 4 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: Apr 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2→47.58 Å / Num. obs: 182621 / % possible obs: 96.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 22 Å2 / CC1/2: 1 / Rpim(I) all: 0.054 / Rsym value: 0.086 / Net I/σ(I): 8.7
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 3.4 / Num. unique obs: 26347 / CC1/2: 0.87 / Rpim(I) all: 0.241 / Rsym value: 0.381 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5M6A

5m6a


Resolution: 2→47.62 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.907 / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28009 9361 5.1 %RANDOM
Rwork0.22909 ---
obs0.23174 173255 96.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.175 Å2
Baniso -1Baniso -2Baniso -3
1--1.08 Å20.03 Å2-0.47 Å2
2---1.95 Å20.62 Å2
3---2.3 Å2
Refinement stepCycle: 1 / Resolution: 2→47.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18744 0 174 1390 20308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01319636
X-RAY DIFFRACTIONr_bond_other_d0.0370.01717019
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.64326882
X-RAY DIFFRACTIONr_angle_other_deg2.4491.57540061
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.07552600
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.37524.555742
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.817152912
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4651541
X-RAY DIFFRACTIONr_chiral_restr0.0650.22649
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0222767
X-RAY DIFFRACTIONr_gen_planes_other0.0090.023684
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_it2.6833.39210337
X-RAY DIFFRACTIONr_mcbond_other2.6833.39210336
X-RAY DIFFRACTIONr_mcangle_it4.0885.06812943
X-RAY DIFFRACTIONr_mcangle_other4.0885.06812944
X-RAY DIFFRACTIONr_scbond_it2.6283.5669299
X-RAY DIFFRACTIONr_scbond_other2.6183.5639273
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0675.23713898
X-RAY DIFFRACTIONr_long_range_B_refined6.75540.15720788
X-RAY DIFFRACTIONr_long_range_B_other6.70239.98720571
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.005→2.057 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 678 -
Rwork0.288 12528 -
obs--93.99 %

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