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- PDB-5m6a: Crystal structure of cardiotoxic Bence-Jones light chain dimer H9 -

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Basic information

Entry
Database: PDB / ID: 5m6a
TitleCrystal structure of cardiotoxic Bence-Jones light chain dimer H9
ComponentsBence-Jones light chain
KeywordsIMMUNE SYSTEM / light chain dimer / light chain amyloidosis / immunoglobulin fold / protein aggregation
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / PHOSPHATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 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 24, 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bence-Jones light chain
B: Bence-Jones light chain
C: Bence-Jones light chain
D: Bence-Jones light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,85211
Polymers90,1994
Non-polymers6537
Water15,889882
1
A: Bence-Jones light chain
B: Bence-Jones light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4736
Polymers45,0992
Non-polymers3744
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-37 kcal/mol
Surface area19610 Å2
MethodPISA
2
C: Bence-Jones light chain
D: Bence-Jones light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3785
Polymers45,0992
Non-polymers2793
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-28 kcal/mol
Surface area19200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.492, 63.429, 86.637
Angle α, β, γ (deg.)95.32, 85.84, 99.58
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody
Bence-Jones light chain


Mass: 22549.658 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Plasmid details: Urine
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 882 / Source method: isolated from a natural source / Formula: H2O

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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: 2.85 Å3/Da / Density % sol: 56.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Sodium citrate, 16 % w/v PEG 4000, 10 % v/v 2-Propanol

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2015
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: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.64→45.77 Å / Num. obs: 113757 / % possible obs: 95.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 22.59 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 7.3
Reflection shellResolution: 1.64→1.7 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.6 / % possible all: 94.2

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JVK

1jvk


Resolution: 1.64→45.77 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.953 / SU R Cruickshank DPI: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.094 / SU Rfree Blow DPI: 0.088 / SU Rfree Cruickshank DPI: 0.086
RfactorNum. reflection% reflectionSelection details
Rfree0.203 5715 5.02 %RANDOM
Rwork0.183 ---
obs0.184 113747 95.7 %-
Displacement parametersBiso mean: 25.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.1756 Å2-0.1579 Å20.4902 Å2
2--0.0102 Å2-0.2228 Å2
3----0.1858 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: 1 / Resolution: 1.64→45.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6235 0 39 882 7156
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016663HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.149138HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2164SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes140HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1000HARMONIC5
X-RAY DIFFRACTIONt_it6663HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.04
X-RAY DIFFRACTIONt_other_torsion15.06
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion897SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8286SEMIHARMONIC4
LS refinement shellResolution: 1.64→1.68 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2649 406 4.91 %
Rwork0.2172 7857 -
all0.2195 8263 -
obs--94.08 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.30390.0787-0.2710.16880.36870.830.0765-0.039-0.0205-0.0167-0.0550.0189-0.0701-0.0909-0.0214-0.01590.03170.0119-0.03240.0216-0.010219.59680.09745.8651
20.16120.0221-0.29120.33590.34611.88650.057-0.01710.03480.01010.002-0.03430.0541-0.0058-0.059-0.04120.023-0.0124-0.01650.0055-0.037334.3905-5.71798.7551
30.20690.0281-0.11440.492-0.1261.41790.010.0245-0.0030.06350.00650.05440.0722-0.0227-0.0165-0.0032-0.01860.0107-0.0621-0.0263-0.054435.864726.7579-32.5617
40.39410.3557-0.26890.7359-0.70181.731-0.01620.052-0.12940.0375-0.0821-0.10270.0760.17720.0983-0.03840.01760.0459-0.0832-0.027-0.014847.957338.0187-29.9827
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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