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- PDB-6mg4: Structure of full-length human lambda-6A light chain JTO -

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Basic information

Entry
Database: PDB / ID: 6mg4
TitleStructure of full-length human lambda-6A light chain JTO
ComponentsJTO light chain
KeywordsIMMUNE SYSTEM / Light chain / amyloidosis
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsMorgan, G.J. / Yan, N.L. / Mortenson, D.E. / Stanfield, R.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: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Stabilization of amyloidogenic immunoglobulin light chains by small molecules.
Authors: Morgan, G.J. / Yan, N.L. / Mortenson, D.E. / Rennella, E. / Blundon, J.M. / Gwin, R.M. / Lin, C.Y. / Stanfield, R.L. / Brown, S.J. / Rosen, H. / Spicer, T.P. / Fernandez-Vega, V. / Merlini, ...Authors: Morgan, G.J. / Yan, N.L. / Mortenson, D.E. / Rennella, E. / Blundon, J.M. / Gwin, R.M. / Lin, C.Y. / Stanfield, R.L. / Brown, S.J. / Rosen, H. / Spicer, T.P. / Fernandez-Vega, V. / Merlini, G. / Kay, L.E. / Wilson, I.A. / Kelly, J.W.
History
DepositionSep 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 1, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 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
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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


Theoretical massNumber of molelcules
Total (without water)46,8602
Polymers46,8602
Non-polymers00
Water11,962664
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-19 kcal/mol
Surface area20170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.385, 82.464, 97.017
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody JTO light chain


Mass: 23429.818 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 664 / Source method: isolated from a natural source / Formula: H2O
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: 2.71 Å3/Da / Density % sol: 54.54 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop
Details: Crystals of JTO-FL were grown via sitting-drop vapor diffusion using a crystallization buffer consisting of 20% PEG 3350 and 0.2 M NH4H2PO4 at 23 degrees C. Both diamond-shaped and plate- ...Details: Crystals of JTO-FL were grown via sitting-drop vapor diffusion using a crystallization buffer consisting of 20% PEG 3350 and 0.2 M NH4H2PO4 at 23 degrees C. Both diamond-shaped and plate-shaped crystals were generated in the same drop using these conditions, but only the plate-shaped crystals produced usable diffraction data. Crystals were harvested and immediately flash cooled in liquid nitrogen.

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.75→44.66 Å / Num. obs: 50814 / % possible obs: 97.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 28 Å2 / CC1/2: 0.96 / Rpim(I) all: 0.034 / Rsym value: 0.055 / Net I/σ(I): 18.2
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2214 / CC1/2: 0.84 / Rpim(I) all: 0.29 / Rsym value: 0.49 / % possible all: 86.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LIL

1lil


Resolution: 1.75→44.66 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.487 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.114 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.221 2560 5 %RANDOM
Rwork0.171 ---
obs0.173 48204 97.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37 Å2
Baniso -1Baniso -2Baniso -3
1--1.82 Å20 Å20 Å2
2--4.41 Å2-0 Å2
3----2.59 Å2
Refinement stepCycle: 1 / Resolution: 1.75→44.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3257 0 0 664 3921
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0153392
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172897
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.7774643
X-RAY DIFFRACTIONr_angle_other_deg0.5431.736854
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1735444
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.15122.424132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.3115483
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5951514
X-RAY DIFFRACTIONr_chiral_restr0.0740.2464
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213859
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02605
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_it3.0343.3821743
X-RAY DIFFRACTIONr_mcbond_other3.0343.3851744
X-RAY DIFFRACTIONr_mcangle_it4.2485.052183
X-RAY DIFFRACTIONr_mcangle_other4.2475.0532184
X-RAY DIFFRACTIONr_scbond_it4.1823.8681649
X-RAY DIFFRACTIONr_scbond_other4.1813.8711650
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4435.5792456
X-RAY DIFFRACTIONr_long_range_B_refined9.42444.6083895
X-RAY DIFFRACTIONr_long_range_B_other9.20342.9543690
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.79 Å
RfactorNum. reflection% reflection
Rfree0.27 175 -
Rwork0.303 3085 -
obs--85.23 %

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