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- PDB-3dvi: Crystal structure of kappa 1 amyloidogenic light chain variable domain -

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Basic information

Entry
Database: PDB / ID: 3dvi
TitleCrystal structure of kappa 1 amyloidogenic light chain variable domain
ComponentsAmyloidogenic light chain variable domain AL-103
KeywordsPROTEIN FIBRIL / AL / light chain amyloidosis / amyloid / immunoglobulin / light chain / light chain variable domain
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsThompson, J.R. / Randles, E.G. / Ramirez-Alvarado, M.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structural alterations within native amyloidogenic immunoglobulin light chains.
Authors: Randles, E.G. / Thompson, J.R. / Martin, D.J. / Ramirez-Alvarado, M.
History
DepositionJul 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: 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

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Assembly

Deposited unit
A: Amyloidogenic light chain variable domain AL-103


Theoretical massNumber of molelcules
Total (without water)11,9721
Polymers11,9721
Non-polymers00
Water3,621201
1
A: Amyloidogenic light chain variable domain AL-103

A: Amyloidogenic light chain variable domain AL-103


Theoretical massNumber of molelcules
Total (without water)23,9452
Polymers23,9452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1340 Å2
ΔGint-11 kcal/mol
Surface area10380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.020, 47.020, 103.356
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-292-

HOH

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Components

#1: Antibody Amyloidogenic light chain variable domain AL-103


Mass: 11972.257 Da / Num. of mol.: 1 / Mutation: N34I, D92H, Q100P, 95ProIns
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 (DE3)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.39 Å3/Da / Density % sol: 48.44 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: Protein: 1.26 mM. Mother Liquor: 15% w/v polyethylene glycol 8000, 0.05 M magnesium acetate, 0.1 M sodium acetate, 0.1 M Tris buffer, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5241 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 20, 2007 / Details: Osmic VariMax optics
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5241 Å / Relative weight: 1
ReflectionResolution: 1.53→103.14 Å / Num. all: 18394 / Num. obs: 16734 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 16.62 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 20.6
Reflection shellResolution: 1.53→1.58 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.365 / % possible all: 35.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2Q20

2q20


Resolution: 1.53→103.14 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.714 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.129 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25144 534 3.2 %RANDOM
Rwork0.18949 ---
all0.19138 18394 --
obs0.19138 16194 91.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.622 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å20 Å2
2---0.4 Å20 Å2
3---0.8 Å2
Refinement stepCycle: LAST / Resolution: 1.53→103.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms916 0 0 202 1118
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.022947
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.881.9661306
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1485127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.392538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.45215152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.859153
X-RAY DIFFRACTIONr_chiral_restr0.1460.2145
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02747
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2180.2504
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.2659
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2158
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.228
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8791.5623
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.5292997
X-RAY DIFFRACTIONr_scbond_it3.6053376
X-RAY DIFFRACTIONr_scangle_it4.764.5309
X-RAY DIFFRACTIONr_rigid_bond_restr2.1283999
X-RAY DIFFRACTIONr_sphericity_free9.0153202
X-RAY DIFFRACTIONr_sphericity_bonded4.0643916
LS refinement shellResolution: 1.53→1.58 Å / Num. reflection Rwork: 387 / Total num. of bins used: 20
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.545910.74563.953636.54326.32012.0938-0.23910.5799-0.1365-1.03320.0465-0.38010.04020.24530.19260.2426-0.135-0.07350.09730.0321-0.0547-13.22532.4271-8.6704
27.2234.8211.61539.31410.19920.4879-0.47080.0140.2217-0.65820.48730.0498-0.15580.0328-0.01650.1486-0.0544-0.02120.09310.00830.0067-6.710914.1512.0674
32.07572.0331.95263.42061.90653.2148-0.1350.03730.1557-0.17990.13590.0825-0.07360.0593-0.00090.0528-0.0007-0.01480.0485-0.02010.016-7.178714.257910.0844
45.9543-0.9381.82025.3249-1.62038.0542-0.21060.21620.1732-0.47150.18560.4576-0.0998-0.17940.0250.0877-0.0526-0.03650.05150.03790.0439-16.4484-1.17581.6972
55.50032.47311.17591.84881.68494.89260.04520.1806-0.4980.08350.3727-0.57070.09430.338-0.41790.02710.00510.0070.0348-0.0650.0962-0.90013.7256.6498
620.58462.1678-8.42789.898-0.504620.29640.55880.10990.00290.04250.3187-0.6311-0.0891.9475-0.8775-0.03770.0417-0.04470.2702-0.23230.14947.01522.76535.691
75.20245.5960.19888.3181.91171.26180.2483-0.1908-0.66530.7693-0.0464-0.71790.1386-0.0191-0.2020.1176-0.0106-0.05470.0130.00360.0611-6.663-0.961810.7413
820.1985-7.68769.92935.3739-4.94626.8262-0.1972-0.2644-0.34720.75570.1131-0.25380.1754-0.06510.08410.2207-0.0092-0.06820.03920.03750.0139-6.2976-3.433915.5895
93.54130.97051.70043.32370.72023.35520.0463-0.2265-0.03870.26320.0139-0.0970.0384-0.0028-0.06020.09830.0044-0.00130.05880.01040.017-7.84464.561414.6061
106.9494.25685.61875.89984.12377.6803-0.0437-0.17260.19220.04440.0904-0.0469-0.03520.0063-0.04670.0590.01270.01220.0578-0.01620.0314-7.930910.139512.8104
112.62852.1571.12694.12591.38612.383-0.20760.1829-0.178-0.14310.4089-0.4809-0.10480.2677-0.20120.0330.00220.01730.0674-0.05460.0705-1.13656.5697.8624
123.70143.49472.72368.38561.60449.41110.05980.3412-0.0188-0.20290.03560.1269-0.30270.1638-0.09550.0538-0.04260.00660.1251-0.05990.0373-11.1224-4.8879-4.8564
139.18439.0441.939111.5102-0.66699.2345-0.47480.5838-0.2505-0.61490.6426-0.46850.06070.1617-0.16780.0611-0.03810.04680.0792-0.05590.0252-2.64769.63920.5232
1415.0933-2.1155-4.982638.94598.477710.4892-0.0001-0.39651.07060.10691.0499-1.5938-1.11130.7206-1.04970.0771-0.0127-0.00110.068-0.11230.07143.813419.228910.479
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 31 - 4
2X-RAY DIFFRACTION2AA4 - 115 - 12
3X-RAY DIFFRACTION3AA12 - 2613 - 27
4X-RAY DIFFRACTION4AA27 - 3328 - 34
5X-RAY DIFFRACTION5AA34 - 3935 - 40
6X-RAY DIFFRACTION6AA40 - 4541 - 46
7X-RAY DIFFRACTION7AA46 - 5147 - 52
8X-RAY DIFFRACTION8AA52 - 5653 - 57
9X-RAY DIFFRACTION9AA57 - 6958 - 70
10X-RAY DIFFRACTION10AA70 - 7871 - 79
11X-RAY DIFFRACTION11AA79 - 9180 - 92
12X-RAY DIFFRACTION12AA92 - 9893 - 99
13X-RAY DIFFRACTION13AA99 - 104100 - 105
14X-RAY DIFFRACTION14AA105 - 108106 - 109

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