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- PDB-3dvf: Structure of amyloidogenic kappa 1 Bence Jones protein -

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Basic information

Entry
Database: PDB / ID: 3dvf
TitleStructure of amyloidogenic kappa 1 Bence Jones protein
ComponentsAmyloidogenic immunoglobulin light chain protein AL-12
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: 1.8 Å
AuthorsRandles, E.G. / Thompson, J.R. / 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 immunoglobulin light chain protein AL-12


Theoretical massNumber of molelcules
Total (without water)11,7371
Polymers11,7371
Non-polymers00
Water1,71195
1
A: Amyloidogenic immunoglobulin light chain protein AL-12

A: Amyloidogenic immunoglobulin light chain protein AL-12


Theoretical massNumber of molelcules
Total (without water)23,4742
Polymers23,4742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area1370 Å2
ΔGint-7 kcal/mol
Surface area10090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.428, 81.428, 77.259
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Antibody Amyloidogenic immunoglobulin light chain protein AL-12


Mass: 11736.984 Da / Num. of mol.: 1 / Mutation: S30T, Y32H, S65R, D70H, E81A, Q91E, N93Y, L96Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Mutant of vk1 o18/o8 germline / Plasmid: pET-12a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 3.15 Å3/Da / Density % sol: 60.95 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: Protein: 923 mM in 10 mM Tris-HCl buffer, pH 7.4. Mother Liquor: 20% w/v polyethylene glycol 4000, 0.2 M Li2SO4, 0.1 M Tris buffer, pH 6.8, under 60% paraffin oil and 40% silicon oil, VAPOR ...Details: Protein: 923 mM in 10 mM Tris-HCl buffer, pH 7.4. Mother Liquor: 20% w/v polyethylene glycol 4000, 0.2 M Li2SO4, 0.1 M Tris buffer, pH 6.8, under 60% paraffin oil and 40% silicon oil, 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: Sep 25, 2007 / Details: Osmic VariMax
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5241 Å / Relative weight: 1
ReflectionResolution: 1.8→77.15 Å / Num. all: 14547 / Num. obs: 13965 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.66 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 17.2
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 3.85 % / Rmerge(I) obs: 3.44 / Mean I/σ(I) obs: 3.3 / Num. unique all: 994 / % possible all: 87.9

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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: 1.8→77.15 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 7.168 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.158 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26566 594 4.1 %RANDOM
Rwork0.19296 ---
all0.19569 14547 --
obs0.19569 13965 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.491 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20.05 Å20 Å2
2--0.09 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.8→77.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms905 0 0 95 1000
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.021938
X-RAY DIFFRACTIONr_angle_refined_deg1.9671.9471294
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0875125
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.55424.87841
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.37915146
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.057153
X-RAY DIFFRACTIONr_chiral_restr0.1350.2139
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02755
X-RAY DIFFRACTIONr_nbd_refined0.2320.2420
X-RAY DIFFRACTIONr_nbtor_refined0.3060.2615
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.269
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2470.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.222
X-RAY DIFFRACTIONr_mcbond_it2.7911.5614
X-RAY DIFFRACTIONr_mcangle_it4.0522975
X-RAY DIFFRACTIONr_scbond_it5.6483378
X-RAY DIFFRACTIONr_scangle_it7.314.5319
LS refinement shellResolution: 1.8→1.85 Å / Num. reflection Rwork: 994 / 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)
126.66217.285612.6044.32823.553613.6863-0.12950.6647-1.4146-0.41750.4345-0.2431-0.73120.327-0.3050.0411-0.0208-0.0398-0.2436-0.0076-0.2715-38.6288.5748-10.3906
20.50912.02970.36349.0037-0.82415.9251-0.0867-1.1530.2188-0.51970.3690.2423-0.5530.6001-0.28220.2886-0.0911-0.06310.2011-0.0834-0.2167-30.224421.15411.2399
332.66977.018620.24065.54217.925519.8892-0.4754-0.36930.9371-0.24420.3649-0.4762-0.9625-0.79180.11040.18960.0945-0.0832-0.3355-0.0129-0.0999-42.685612.2818-10.241
411.9201-1.667618.70141.4674-5.123634.4346-0.03-0.8544-0.4118-0.25420.18250.6579-0.2963-2.2044-0.1525-0.01240.0917-0.12930.0457-0.0975-0.0192-51.99088.8803-6.5084
52.949-4.4043-0.12299.0122-1.03018.416-0.18750.2089-0.38580.05380.11280.6282-0.4476-0.05450.0747-0.1802-0.0132-0.0172-0.3410.0022-0.2742-39.29967.12421.9786
631.6251-5.19799.432910.0719-0.79720.65230.02-0.5076-0.62710.6081-0.0672-0.4389-0.0190.95950.0472-0.1643-0.0291-0.0476-0.27210.0045-0.2445-33.77392.47686.6218
729.3084-17.926418.051622.0201-5.075814.3372-0.3314-0.5462-0.5173-0.4468-0.34131.0967-0.8907-1.15190.6726-0.06530.13080.0165-0.1132-0.03-0.1831-47.639410.62213.9022
819.60251.20338.64413.29191.616146.41890.0484-0.64-0.03170.70510.13141.4166-0.5958-0.4624-0.1798-0.01520.06730.0751-0.0749-0.0841-0.1165-46.467511.915310.1565
926.1374-0.022918.79917.75265.860317.976-0.4593-0.29360.6112-0.8803-0.2750.0294-1.3038-0.36480.73440.07560.0852-0.0857-0.1867-0.0872-0.182-41.822917.92284.7257
104.20030.53312.93033.6531.89097.0159-0.2656-0.38940.1184-0.2824-0.02290.2478-1.1221-0.37160.28850.02590.0198-0.0292-0.2662-0.0144-0.3041-39.375312.6613-0.2336
1148.8319-5.9418-10.175215.95935.907825.70220.62140.9263-2.2308-0.3249-0.73092.28820.7026-2.69870.1095-0.0402-0.0367-0.13390.0199-0.05250.1027-49.5669-0.3724-7.7109
1219.455413.77771.595718.23415.11678.8456-0.0418-0.9069-0.53720.13590.3875-1.0956-0.96421.5173-0.34580.0499-0.0875-0.041-0.0306-0.0291-0.316-30.377610.7099-1.9548
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 111 - 11
2X-RAY DIFFRACTION2AA12 - 2012 - 20
3X-RAY DIFFRACTION3AA21 - 2621 - 26
4X-RAY DIFFRACTION4AA27 - 3427 - 34
5X-RAY DIFFRACTION5AA35 - 3835 - 38
6X-RAY DIFFRACTION6AA39 - 4539 - 45
7X-RAY DIFFRACTION7AA46 - 5246 - 52
8X-RAY DIFFRACTION8AA53 - 5853 - 58
9X-RAY DIFFRACTION9AA59 - 6659 - 66
10X-RAY DIFFRACTION10AA67 - 9167 - 91
11X-RAY DIFFRACTION11AA92 - 9792 - 97
12X-RAY DIFFRACTION12AA98 - 10798 - 107

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