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- PDB-6dj0: ASLTVS segment from Human Immunoglobulin Light-Chain Variable Dom... -

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Basic information

Entry
Database: PDB / ID: 6dj0
TitleASLTVS segment from Human Immunoglobulin Light-Chain Variable Domain, Residues 73-78, assembled as an amyloid fibril
ComponentsASLTVS segment from Light-Chain Variable Domain, Lambda Mcg
KeywordsPROTEIN FIBRIL / amyloid fibril
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
Model detailsamyloid fibril
AuthorsBrumshtein, B. / Esswein, S.R. / Sawaya, M.R. / Eisenberg, D.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)1R01AG048120-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41 GM103403 United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Identification of two principal amyloid-driving segments in variable domains of Ig light chains in systemic light-chain amyloidosis.
Authors: Brumshtein, B. / Esswein, S.R. / Sawaya, M.R. / Rosenberg, G. / Ly, A.T. / Landau, M. / Eisenberg, D.S.
History
DepositionMay 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ASLTVS segment from Light-Chain Variable Domain, Lambda Mcg
B: ASLTVS segment from Light-Chain Variable Domain, Lambda Mcg


Theoretical massNumber of molelcules
Total (without water)1,1532
Polymers1,1532
Non-polymers00
Water1086
1
A: ASLTVS segment from Light-Chain Variable Domain, Lambda Mcg
B: ASLTVS segment from Light-Chain Variable Domain, Lambda Mcg

A: ASLTVS segment from Light-Chain Variable Domain, Lambda Mcg
B: ASLTVS segment from Light-Chain Variable Domain, Lambda Mcg

A: ASLTVS segment from Light-Chain Variable Domain, Lambda Mcg
B: ASLTVS segment from Light-Chain Variable Domain, Lambda Mcg

A: ASLTVS segment from Light-Chain Variable Domain, Lambda Mcg
B: ASLTVS segment from Light-Chain Variable Domain, Lambda Mcg


Theoretical massNumber of molelcules
Total (without water)4,6138
Polymers4,6138
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation2_556-x,y+1/2,-z+11
crystal symmetry operation2_546-x,y-1/2,-z+11
Unit cell
Length a, b, c (Å)15.167, 11.580, 18.798
Angle α, β, γ (deg.)90.000, 97.320, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide ASLTVS segment from Light-Chain Variable Domain, Lambda Mcg


Mass: 576.641 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 1.42 Å3/Da / Density % sol: 13.36 % / Mosaicity: 0.6 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1 M Malic Acid, MES:Tris buffer, 25% PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.3→100 Å / Num. obs: 1351 / % possible obs: 80.5 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.192 / Χ2: 1.034 / Net I/σ(I): 5.6 / Num. measured all: 3352
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.3-1.41.50.272071.042162.5
1.4-1.541.70.3012070.963164.9
1.54-1.761.90.42461.059174.3
1.76-2.223.20.2933331.052198.2
2.22-1003.20.1333581.0221100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IDEAL beta strand

Resolution: 1.3→18.64 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.9 / SU ML: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.09
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.218 130 9.7 %RANDOM
Rwork0.1826 ---
obs0.1861 1215 79.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 24.06 Å2 / Biso mean: 6.422 Å2 / Biso min: 3.48 Å2
Baniso -1Baniso -2Baniso -3
1-1.8 Å2-0 Å20.12 Å2
2---0.61 Å20 Å2
3----1.17 Å2
Refinement stepCycle: final / Resolution: 1.3→18.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms80 0 0 6 86
Biso mean---12.87 -
Num. residues----12
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0291
X-RAY DIFFRACTIONr_bond_other_d0.0060.02103
X-RAY DIFFRACTIONr_angle_refined_deg2.0852.106124
X-RAY DIFFRACTIONr_angle_other_deg0.9543235
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.466512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.1651515
X-RAY DIFFRACTIONr_chiral_restr0.1320.221
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0292
X-RAY DIFFRACTIONr_gen_planes_other00.0212
LS refinement shellResolution: 1.301→1.453 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.328 32 -
Rwork0.323 258 -
all-290 -
obs--61.44 %

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