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- PDB-2q1e: Altered dimer interface decreases stability in an amyloidogenic k... -

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Basic information

Entry
Database: PDB / ID: 2q1e
TitleAltered dimer interface decreases stability in an amyloidogenic kappa1 Bence Jones protein.
ComponentsAmyloidogenic immunoglobulin light chain protein AL-09
KeywordsPROTEIN FIBRIL / AL / light chain amyloidosis / amyloid / immunoglobulin / light chain / light chain variable domain
Function / homology
Function and homology information


Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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: 2.55 Å
AuthorsThompson, J.R. / Ramirez-Alvarado, M. / Baden, E.M.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Altered dimer interface decreases stability in an amyloidogenic protein.
Authors: Baden, E.M. / Owen, B.A. / Peterson, F.C. / Volkman, B.F. / Ramirez-Alvarado, M. / Thompson, J.R.
History
DepositionMay 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999sequence The sequence is not available in the UniProt database at the time of processing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amyloidogenic immunoglobulin light chain protein AL-09
B: Amyloidogenic immunoglobulin light chain protein AL-09
C: Amyloidogenic immunoglobulin light chain protein AL-09
D: Amyloidogenic immunoglobulin light chain protein AL-09
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9215
Polymers47,8254
Non-polymers961
Water7,981443
1
A: Amyloidogenic immunoglobulin light chain protein AL-09
B: Amyloidogenic immunoglobulin light chain protein AL-09
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0083
Polymers23,9122
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Amyloidogenic immunoglobulin light chain protein AL-09
D: Amyloidogenic immunoglobulin light chain protein AL-09


Theoretical massNumber of molelcules
Total (without water)23,9122
Polymers23,9122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)176.054, 176.054, 176.054
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-501-

SO4

21A-501-

SO4

31A-270-

HOH

41D-258-

HOH

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Components

#1: Antibody
Amyloidogenic immunoglobulin light chain protein AL-09


Mass: 11956.148 Da / Num. of mol.: 4 / Mutation: S30N, N34I, K42Q, N53T, D70E, I83L, Y87H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: mutant of Vk1 O18/O8 germline / Plasmid: pET12a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold / References: UniProt: A2NI60
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 443 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.75 Å3/Da / Density % sol: 74.11 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: Mother Liquor: 15-30% (w/v) PEG 4K, 0.2 M Li2SO4, 0.1 M TRIS pH 7.9-8.9. Protein: 890 micromolar in 10 mM TRIS, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.0718 Å
DetectorType: SBC-3 / Detector: CCD / Date: Feb 7, 2007 / Details: mirror
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0718 Å / Relative weight: 1
ReflectionResolution: 2.55→176 Å / Num. all: 29819 / Num. obs: 29819 / % possible obs: 99.3 % / Redundancy: 98.7 % / Biso Wilson estimate: 50.3 Å2 / Rsym value: 0.095 / Net I/σ(I): 82.5
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 68.3 % / Mean I/σ(I) obs: 9.8 / Num. unique all: 2094 / Rsym value: 0.47 / % possible all: 93

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Vk1 O18/O8 germline variable light chain domain monomer

Resolution: 2.55→35.21 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.935 / SU B: 10.919 / SU ML: 0.132 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20601 529 1.7 %RANDOM
Rwork0.16547 ---
obs0.1662 29819 97.73 %-
all-29819 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.458 Å2
Refinement stepCycle: LAST / Resolution: 2.55→35.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3490 0 5 443 3938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223582
X-RAY DIFFRACTIONr_bond_other_d0.0010.022341
X-RAY DIFFRACTIONr_angle_refined_deg1.8321.9614898
X-RAY DIFFRACTIONr_angle_other_deg1.2923.0035774
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0265459
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.9325.949158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.46515585
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.731158
X-RAY DIFFRACTIONr_chiral_restr0.0970.2546
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024081
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02671
X-RAY DIFFRACTIONr_nbd_refined0.2050.2610
X-RAY DIFFRACTIONr_nbd_other0.2170.22422
X-RAY DIFFRACTIONr_nbtor_refined0.1880.21724
X-RAY DIFFRACTIONr_nbtor_other0.0950.22052
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2301
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0550.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3440.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2350.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8291.52861
X-RAY DIFFRACTIONr_mcbond_other0.1721.5906
X-RAY DIFFRACTIONr_mcangle_it1.16123689
X-RAY DIFFRACTIONr_scbond_it2.14531547
X-RAY DIFFRACTIONr_scangle_it3.3164.51209
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 39 -
Rwork0.242 2094 -
obs--95.44 %

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