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- PDB-6dix: NFVFGT segment from Human Immunoglobulin Light-Chain Variable Dom... -

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Basic information

Entry
Database: PDB / ID: 6dix
TitleNFVFGT segment from Human Immunoglobulin Light-Chain Variable Domain, Residues 98-103, assembled as an amyloid fibril
ComponentsNFVFGT Immunoglobulin Light-Chain Variable Domain
KeywordsPROTEIN FIBRIL / amyloid fibril
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1 Å
Model detailsNFVFGT segment from Human Immunoglobulin Light-Chain Variable Domain, Residues 98-103, assembled as ...NFVFGT segment from Human Immunoglobulin Light-Chain Variable Domain, Residues 98-103, assembled as an amyloid 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 23, 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 1.4Jan 15, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.5Mar 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NFVFGT Immunoglobulin Light-Chain Variable Domain
B: NFVFGT Immunoglobulin Light-Chain Variable Domain
C: NFVFGT Immunoglobulin Light-Chain Variable Domain
D: NFVFGT Immunoglobulin Light-Chain Variable Domain


Theoretical massNumber of molelcules
Total (without water)2,7354
Polymers2,7354
Non-polymers00
Water32418
1
A: NFVFGT Immunoglobulin Light-Chain Variable Domain
B: NFVFGT Immunoglobulin Light-Chain Variable Domain
C: NFVFGT Immunoglobulin Light-Chain Variable Domain
D: NFVFGT Immunoglobulin Light-Chain Variable Domain

A: NFVFGT Immunoglobulin Light-Chain Variable Domain
B: NFVFGT Immunoglobulin Light-Chain Variable Domain
C: NFVFGT Immunoglobulin Light-Chain Variable Domain
D: NFVFGT Immunoglobulin Light-Chain Variable Domain

A: NFVFGT Immunoglobulin Light-Chain Variable Domain
B: NFVFGT Immunoglobulin Light-Chain Variable Domain
C: NFVFGT Immunoglobulin Light-Chain Variable Domain
D: NFVFGT Immunoglobulin Light-Chain Variable Domain

A: NFVFGT Immunoglobulin Light-Chain Variable Domain
B: NFVFGT Immunoglobulin Light-Chain Variable Domain
C: NFVFGT Immunoglobulin Light-Chain Variable Domain
D: NFVFGT Immunoglobulin Light-Chain Variable Domain


Theoretical massNumber of molelcules
Total (without water)10,94016
Polymers10,94016
Non-polymers00
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_445x-1,y-1,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_455x-1,y,z1
Unit cell
Length a, b, c (Å)16.030, 11.660, 21.940
Angle α, β, γ (deg.)90.890, 103.230, 90.260
Int Tables number1
Space group name H-MP1

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Components

#1: Protein/peptide
NFVFGT Immunoglobulin Light-Chain Variable Domain


Mass: 683.752 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 1.46 Å3/Da / Density % sol: 15.72 % / Description: rod
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Imidazole, 20% PEG 3000, 0.2 M Zinc Acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9717 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 6, 2015
RadiationMonochromator: Cryo-cooled-double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9717 Å / Relative weight: 1
ReflectionResolution: 1→21.35 Å / Num. obs: 6835 / % possible obs: 81.8 % / Redundancy: 3.424 % / Biso Wilson estimate: 8.571 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.077 / Χ2: 1.025 / Net I/σ(I): 12.83
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1-1.073.1770.1246.739260.9820.14860.4
1.07-2.33.4460.06813.0952950.9960.0886.2
2.3-33.6110.05919.813370.9970.06991.3
3-53.5880.06519.82110.9960.07686.1
5-83.6730.04820.22520.9990.057100
8-103.3330.11119.260.9640.12975
10-21.353.50.04320.2380.9980.05100

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Processing

Software
NameVersionClassification
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
SHELXDphasing
RefinementMethod to determine structure: AB INITIO PHASING
Starting model: NO Starting model, We used DIRECT METHODS

Resolution: 1→21.35 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.971 / SU R Cruickshank DPI: 0.0262 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.026 / ESU R Free: 0.026
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1247 684 10 %RANDOM
Rwork0.1025 ---
obs0.1048 6154 81.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 35.6 Å2 / Biso mean: 7.488 Å2 / Biso min: 2.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å2-0.24 Å2-0.18 Å2
2---0.03 Å2-0.02 Å2
3---0.45 Å2
Refinement stepCycle: final / Resolution: 1→21.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms196 0 0 18 214
Biso mean---21.32 -
Num. residues----24
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.013210
X-RAY DIFFRACTIONr_bond_other_d00.018184
X-RAY DIFFRACTIONr_angle_refined_deg1.5891.688286
X-RAY DIFFRACTIONr_angle_other_deg1.4771.685418
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.046524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.96923.33312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.471522
X-RAY DIFFRACTIONr_chiral_restr0.0860.226
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02242
X-RAY DIFFRACTIONr_gen_planes_other0.010.0262
X-RAY DIFFRACTIONr_rigid_bond_restr20.2793394
X-RAY DIFFRACTIONr_sphericity_free17.74159
X-RAY DIFFRACTIONr_sphericity_bonded6.4475397
LS refinement shellResolution: 1→1.026 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.123 28 -
Rwork0.145 249 -
all-277 -
obs--46.71 %

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