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- PDB-9fvk: Crystal structure of amyloidogenic light chain AL-55 in open conf... -

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Open data


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Basic information

Entry
Database: PDB / ID: 9fvk
TitleCrystal structure of amyloidogenic light chain AL-55 in open conformation.
ComponentsAL55
KeywordsIMMUNE SYSTEM / Light chain / amyloidosis
Function / homologyDI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsPolsinelli, I. / Puri, S. / Broggini, L. / Gadda, A. / Petralia, U. / Ricagno, S.
Funding support Italy, 1items
OrganizationGrant numberCountry
University and Research - University of Milan Italy
CitationJournal: To Be Published
Title: To be published
Authors: Puri, S. / Polsinelli, I. / Ricagno, S.
History
DepositionJun 27, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AL55
B: AL55
C: AL55
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,60610
Polymers69,9803
Non-polymers6267
Water1,802100
1
A: AL55
B: AL55
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0897
Polymers46,6532
Non-polymers4365
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-37 kcal/mol
Surface area21700 Å2
MethodPISA
2
C: AL55
hetero molecules

C: AL55
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0336
Polymers46,6532
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2720 Å2
ΔGint-28 kcal/mol
Surface area21510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.817, 208.381, 72.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Antibody , 1 types, 3 molecules ABC

#1: Antibody AL55


Mass: 23326.557 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 6 types, 107 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 3 Å3/Da / Density % sol: 58.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 0.1 M MIB (Sodium malonate dibasic monohydrate, Imidazole, Boric acid) pH 5.0, and 25 % w/v PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Apr 4, 2023
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.64→45.64 Å / Num. obs: 25185 / % possible obs: 99.88 % / Redundancy: 13.8 % / Biso Wilson estimate: 54.64 Å2 / CC1/2: 0.987 / Rrim(I) all: 0.3629 / Net I/σ(I): 6.27
Reflection shellResolution: 2.64→2.73 Å / Num. unique obs: 2478 / CC1/2: 0.856

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
BUSTERrefinement
REFMAC5.0.32refinement
EDNAdata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.64→45.64 Å / SU ML: 0.3811 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.1221
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2253 1280 5.08 %
Rwork0.1937 23893 -
obs0.1954 25173 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.37 Å2
Refinement stepCycle: LAST / Resolution: 2.64→45.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4902 0 37 100 5039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00225072
X-RAY DIFFRACTIONf_angle_d0.57346925
X-RAY DIFFRACTIONf_chiral_restr0.0434773
X-RAY DIFFRACTIONf_plane_restr0.0044895
X-RAY DIFFRACTIONf_dihedral_angle_d6.755700
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.64-2.750.37441390.32012613X-RAY DIFFRACTION100
2.75-2.870.34171400.27282628X-RAY DIFFRACTION99.96
2.87-3.020.25971380.24532625X-RAY DIFFRACTION99.82
3.02-3.210.28331190.24012633X-RAY DIFFRACTION99.89
3.21-3.460.27741250.21982649X-RAY DIFFRACTION99.89
3.46-3.810.26011680.19032624X-RAY DIFFRACTION99.82
3.81-4.360.18721570.16532630X-RAY DIFFRACTION99.96
4.36-5.490.1781500.15172681X-RAY DIFFRACTION100

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