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- PDB-5mtl: Crystal structure of an amyloidogenic light chain -

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Basic information

Entry
Database: PDB / ID: 5mtl
TitleCrystal structure of an amyloidogenic light chain
Componentslight chain dimer,IGL@ protein,IGL@ protein
KeywordsIMMUNE SYSTEM / light chain dimer / light chain amyloidosis / immunoglobulin fold / protein aggregation
Function / homology
Function and homology information


Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsOberti, L. / Rognoni, P. / Russo, R. / 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
DepositionJan 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_validate_close_contact ...pdbx_data_processing_status / pdbx_validate_close_contact / struct_conn / struct_conn_type
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: light chain dimer,IGL@ protein,IGL@ protein
B: light chain dimer,IGL@ protein,IGL@ protein
C: light chain dimer,IGL@ protein,IGL@ protein
D: light chain dimer,IGL@ protein,IGL@ protein


Theoretical massNumber of molelcules
Total (without water)91,0244
Polymers91,0244
Non-polymers00
Water79344
1
A: light chain dimer,IGL@ protein,IGL@ protein
B: light chain dimer,IGL@ protein,IGL@ protein


Theoretical massNumber of molelcules
Total (without water)45,5122
Polymers45,5122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-16 kcal/mol
Surface area19190 Å2
MethodPISA
2
C: light chain dimer,IGL@ protein,IGL@ protein
D: light chain dimer,IGL@ protein,IGL@ protein


Theoretical massNumber of molelcules
Total (without water)45,5122
Polymers45,5122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-17 kcal/mol
Surface area19340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.484, 65.085, 88.386
Angle α, β, γ (deg.)84.96, 86.66, 79.93
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody
light chain dimer,IGL@ protein,IGL@ protein


Mass: 22756.051 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGL@ / Production host: Escherichia coli (E. coli) / References: UniProt: Q567P1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.88 Å3/Da / Density % sol: 57.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Sodium cacodylate, 27% w/v PEG 2000 MME

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Data collection

DiffractionMean temperature: 126.15 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.45→28.57 Å / Num. obs: 36581 / % possible obs: 98.2 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 8.8
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3606 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
SCALAdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M6I

5m6i


Resolution: 2.45→29.289 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 31.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2768 1826 4.99 %
Rwork0.2342 --
obs0.2363 36581 98.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→29.289 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5921 0 0 44 5965
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046045
X-RAY DIFFRACTIONf_angle_d0.858262
X-RAY DIFFRACTIONf_dihedral_angle_d13.0023634
X-RAY DIFFRACTIONf_chiral_restr0.05943
X-RAY DIFFRACTIONf_plane_restr0.0061069
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.51620.30981320.31272633X-RAY DIFFRACTION98
2.5162-2.59020.37521340.32252694X-RAY DIFFRACTION98
2.5902-2.67380.35211230.30832659X-RAY DIFFRACTION98
2.6738-2.76930.36561530.312676X-RAY DIFFRACTION98
2.7693-2.880.36111410.30092684X-RAY DIFFRACTION98
2.88-3.0110.31851250.28452642X-RAY DIFFRACTION98
3.011-3.16960.33431440.27842699X-RAY DIFFRACTION98
3.1696-3.36790.30991360.25772655X-RAY DIFFRACTION98
3.3679-3.62750.27971400.22962711X-RAY DIFFRACTION98
3.6275-3.99170.27291330.22162664X-RAY DIFFRACTION98
3.9917-4.56740.21761480.17432706X-RAY DIFFRACTION99
4.5674-5.74740.20341610.16982669X-RAY DIFFRACTION99
5.7474-29.29140.23481560.1942663X-RAY DIFFRACTION98

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