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- PDB-5m76: Crystal structure of cardiotoxic Bence-Jones light chain dimer H10 -

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Basic information

Entry
Database: PDB / ID: 5m76
TitleCrystal structure of cardiotoxic Bence-Jones light chain dimer H10
Componentslight chain dimer
KeywordsIMMUNE SYSTEM / light chain dimer / light chain amyloidosis / immunoglobulin fold / protein aggregation
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / BROMIDE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsOberti, L. / Rognoni, P. / Bacarizo, J. / Bolognesi, M. / Ricagno, S.
CitationJournal: Sci Rep / Year: 2017
Title: Concurrent structural and biophysical traits link with immunoglobulin light chains amyloid propensity.
Authors: Oberti, L. / Rognoni, P. / Barbiroli, A. / Lavatelli, F. / Russo, R. / Maritan, M. / Palladini, G. / Bolognesi, M. / Merlini, G. / Ricagno, S.
History
DepositionOct 26, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 17, 2024Group: 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 1.3Oct 23, 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: light chain dimer
B: light chain dimer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2483
Polymers45,1682
Non-polymers801
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-22 kcal/mol
Surface area18490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.493, 71.417, 103.929
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 light chain dimer


Mass: 22583.920 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Plasmid details: Urine
#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.13 Å3/Da / Density % sol: 42.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.05M KBr, 30% PEG 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2016
RadiationMonochromator: Si(111) and Si(311) liquid nitrogen cooled channel-cut silicon monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.5→48.95 Å / Num. obs: 14761 / % possible obs: 99.2 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 8.6
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.3 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M6A

5m6a


Resolution: 2.5→48.95 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.42
RfactorNum. reflection% reflection
Rfree0.2824 730 4.97 %
Rwork0.2387 --
obs0.241 14684 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→48.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3110 0 1 49 3160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023172
X-RAY DIFFRACTIONf_angle_d0.5954342
X-RAY DIFFRACTIONf_dihedral_angle_d13.5341902
X-RAY DIFFRACTIONf_chiral_restr0.045506
X-RAY DIFFRACTIONf_plane_restr0.005556
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.69310.39361230.33982705X-RAY DIFFRACTION97
2.6931-2.96410.37381440.31012759X-RAY DIFFRACTION99
2.9641-3.39290.35451630.27242755X-RAY DIFFRACTION99
3.3929-4.27430.28261450.22122808X-RAY DIFFRACTION99
4.2743-48.96120.19611550.18922927X-RAY DIFFRACTION99

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