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- PDB-5mud: Crystal structure of an amyloidogenic light chain dimer H6 -

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Basic information

Entry
Database: PDB / ID: 5mud
TitleCrystal structure of an amyloidogenic light chain dimer H6
Componentslight chain dimer,IGL@ protein
KeywordsIMMUNE SYSTEM / light chain dimer / light chain amyloidosis / immunoglobulin fold / protein aggregation
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsOberti, L. / Bacarizo, J. / Maritan, M. / Rognoni, P. / 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
DepositionJan 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength
Revision 1.2Oct 16, 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,IGL@ protein
B: light chain dimer,IGL@ protein


Theoretical massNumber of molelcules
Total (without water)45,5262
Polymers45,5262
Non-polymers00
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2910 Å2
ΔGint-16 kcal/mol
Surface area19760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.055, 72.810, 84.992
Angle α, β, γ (deg.)90.00, 105.29, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Antibody light chain dimer,IGL@ protein


Mass: 22763.221 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.: 22 / 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: 2.62 Å3/Da / Density % sol: 53.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bicine pH 9.0, 2% w/v 1,4-Dioxane, 10% w/v PEG 20K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97895 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 2.34→52.98 Å / Num. obs: 19281 / % possible obs: 96 % / Redundancy: 3.3 % / Biso Wilson estimate: 58.48 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 16.6
Reflection shellResolution: 2.34→2.42 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.512 / Num. unique obs: 1908 / % possible all: 95.8

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M6I

5m6i


Resolution: 2.34→52.98 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.922 / SU R Cruickshank DPI: 0.335 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.313 / SU Rfree Blow DPI: 0.23 / SU Rfree Cruickshank DPI: 0.239
RfactorNum. reflection% reflectionSelection details
Rfree0.249 892 4.64 %RANDOM
Rwork0.205 ---
obs0.207 19222 96.1 %-
Displacement parametersBiso mean: 59.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.909 Å20 Å2-0.4283 Å2
2---0.7849 Å20 Å2
3----0.1242 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: 1 / Resolution: 2.34→52.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3127 0 0 22 3149
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013210HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.244382HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1038SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes66HARMONIC2
X-RAY DIFFRACTIONt_gen_planes468HARMONIC5
X-RAY DIFFRACTIONt_it3210HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.03
X-RAY DIFFRACTIONt_other_torsion18.84
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion436SEMIHARMONIC5
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_contact3379SEMIHARMONIC4
LS refinement shellResolution: 2.34→2.47 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2972 149 5.29 %
Rwork0.2363 2669 -
all0.2396 2818 -
obs--97.67 %

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