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- PDB-8fo5: Structure of full-length amyloidogenic immunoglobulin light chain... -

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Basic information

Entry
Database: PDB / ID: 8fo5
TitleStructure of full-length amyloidogenic immunoglobulin light chain H9 in complex with 1-(1-(phenylsulfonyl)-1H-pyrrol-3-yl)ethan-1-one
ComponentsH9 immunoglobulin light chain
KeywordsIMMUNE SYSTEM / light chain / amyloidosis / stabilizer
Function / homologyPHOSPHATE ION / 1-[1-(benzenesulfonyl)-1H-pyrrol-3-yl]ethan-1-one
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,07710
Polymers90,1994
Non-polymers8786
Water19,2221067
1
A: H9 immunoglobulin light chain
B: H9 immunoglobulin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5395
Polymers45,0992
Non-polymers4393
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-29 kcal/mol
Surface area19800 Å2
MethodPISA
2
C: H9 immunoglobulin light chain
D: H9 immunoglobulin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5395
Polymers45,0992
Non-polymers4393
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-30 kcal/mol
Surface area19750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.674, 63.568, 87.242
Angle α, β, γ (deg.)84.39, 85.51, 80.09
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.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-Y4U / 1-[1-(benzenesulfonyl)-1H-pyrrol-3-yl]ethan-1-one


Mass: 249.286 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H11NO3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 1067 / 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: 2.81 Å3/Da / Density % sol: 56.19 %
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: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.89→48.69 Å / Num. obs: 74530 / % possible obs: 95.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 23 Å2 / CC1/2: 1 / Rpim(I) all: 0.047 / Rsym value: 0.073 / Net I/σ(I): 10.9
Reflection shellResolution: 1.89→2 Å / Mean I/σ(I) obs: 2.9 / Num. unique obs: 9836 / CC1/2: 0.85 / Rpim(I) all: 0.275 / Rsym value: 0.437

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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: 1.89→48.73 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.921 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25028 3736 5 %RANDOM
Rwork0.20121 ---
obs0.20367 70774 95.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.964 Å2
Baniso -1Baniso -2Baniso -3
1-1.56 Å20.16 Å21.64 Å2
2---0.93 Å20.3 Å2
3----0.26 Å2
Refinement stepCycle: 1 / Resolution: 1.89→48.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6310 0 54 1067 7431
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0136578
X-RAY DIFFRACTIONr_bond_other_d0.0370.0175688
X-RAY DIFFRACTIONr_angle_refined_deg1.5821.6449005
X-RAY DIFFRACTIONr_angle_other_deg2.4481.57313397
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8425872
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.40824.839248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02715977
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7231512
X-RAY DIFFRACTIONr_chiral_restr0.070.2887
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027599
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021221
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_it2.4172.7153467
X-RAY DIFFRACTIONr_mcbond_other2.4142.7133466
X-RAY DIFFRACTIONr_mcangle_it3.7054.0524343
X-RAY DIFFRACTIONr_mcangle_other3.7054.0554344
X-RAY DIFFRACTIONr_scbond_it2.8632.9613111
X-RAY DIFFRACTIONr_scbond_other2.8042.9523095
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3384.3034636
X-RAY DIFFRACTIONr_long_range_B_refined7.02333.6687445
X-RAY DIFFRACTIONr_long_range_B_other6.7432.7467120
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.895→1.944 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 244 -
Rwork0.33 4504 -
obs--81.86 %

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