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- PDB-3u7a: AL-09 Y32F Y96F -

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Basic information

Entry
Database: PDB / ID: 3u7a
TitleAL-09 Y32F Y96F
ComponentsAmyloidogenic immunoglobulin light chain protein AL-09 Y32F Y96F, variable domain
KeywordsIMMUNE SYSTEM / immunoglobulin 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: 2 Å
AuthorsDiCostanzo, A.C. / Thompson, J.R. / Ramirez-Alvarado, M.
CitationJournal: To be Published
Title: Tyrosine Residues mediate crucial interactions in amyloid formation for immunoglobulin light chains
Authors: DiCostanzo, A.C. / Thompson, J.R. / Peterson, F.C. / Volkman, B.F. / Ramirez-Alvarado, M.
History
DepositionOct 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Amyloidogenic immunoglobulin light chain protein AL-09 Y32F Y96F, variable domain


Theoretical massNumber of molelcules
Total (without water)12,0971
Polymers12,0971
Non-polymers00
Water2,144119
1
A: Amyloidogenic immunoglobulin light chain protein AL-09 Y32F Y96F, variable domain

A: Amyloidogenic immunoglobulin light chain protein AL-09 Y32F Y96F, variable domain


Theoretical massNumber of molelcules
Total (without water)24,1952
Polymers24,1952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area1450 Å2
ΔGint-15 kcal/mol
Surface area9580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.120, 52.120, 156.470
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-154-

HOH

21A-176-

HOH

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Components

#1: Antibody Amyloidogenic immunoglobulin light chain protein AL-09 Y32F Y96F, variable domain


Mass: 12097.342 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.54 Å3/Da / Density % sol: 51.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 27% (w/v) polyethylene glycol 4000 and 0.15 M Li2SO4 in 0.1 M Tris HCl pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 2, 2011
RadiationMonochromator: Osmic VariMax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→60 Å / Num. obs: 7792 / % possible obs: 85 % / Observed criterion σ(F): 4.11 / Observed criterion σ(I): 16.9
Reflection shellResolution: 2→2.08 Å / % possible all: 31.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→39.1 Å / SU ML: 0.46 / σ(F): 1.35 / Phase error: 23.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.232 439 5.68 %
Rwork0.201 --
obs0.203 7727 84.9 %
Solvent computationShrinkage radii: 0.53 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.61 Å2 / ksol: 0.45 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.9308 Å20 Å20 Å2
2--3.9308 Å2-0 Å2
3----7.8616 Å2
Refinement stepCycle: LAST / Resolution: 2→39.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms826 0 0 119 945
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006926
X-RAY DIFFRACTIONf_angle_d0.9511270
X-RAY DIFFRACTIONf_dihedral_angle_d14.937351
X-RAY DIFFRACTIONf_chiral_restr0.058143
X-RAY DIFFRACTIONf_plane_restr0.005170
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.29450.27231090.2421659X-RAY DIFFRACTION61
2.2945-2.89070.30471580.21192637X-RAY DIFFRACTION94
2.8907-39.10430.20241720.19232992X-RAY DIFFRACTION99
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)
18.38464.33530.53058.08091.72335.5718-0.03190.51951.0317-1.11160.35081.0599-0.5257-0.5146-0.26960.35070.0701-0.0210.39240.05410.2922-15.274318.8177-0.8812
23.5242-1.80713.88657.1558-3.18764.55360.08470.412-0.0427-0.3607-0.0923-0.094-0.05790.1848-0.04650.37020.01450.01890.30450.00510.1643-19.3554-2.04184.7184
36.11666.4643-3.6439.0510.35242.0078-0.4147-0.24720.1476-0.12010.33230.29620.0318-0.43140.2330.44980.0446-0.00410.30720.01750.2091-13.27687.90991.9176
42.03621.6912-1.00515.6137-2.30422.02980.2847-0.02030.2252-0.0604-0.4085-0.5853-0.97041.78020.34880.3649-0.11740.06340.4848-0.03040.312-5.219619.52233.3312
56.74546.4713-3.52426.229-3.8369.9756-0.0817-0.20210.08760.30010.02110.2270.10660.2295-0.00710.21560.05160.02260.21620.01080.2802-18.550411.530812.0019
63.53090.77510.20037.31754.06673.68170.2828-0.7721-0.24180.5796-0.34550.9330.0771-0.67520.07850.4206-0.0070.08510.49940.10990.335-20.944310.940816.5529
71.49141.3910.07182.6837-0.59461.09450.0999-0.1006-0.05230.0861-0.1014-0.11510.03590.1033-0.01130.26870.02240.01250.2333-0.02670.1935-12.88056.85311.3319
84.20261.5896-0.15059.2231-1.22290.1751-0.42310.19550.129-0.47570.0898-0.03260.0634-0.17870.42070.39880.01920.05420.3456-0.01120.1903-14.23921.94445.9712
95.2375-0.9969-1.58238.7623-6.14985.3512-0.5613-0.1957-0.6007-1.37260.56360.53180.4987-1.09820.070.555-0.0709-0.03580.4618-0.06930.3359-25.45270.6286.5355
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:7)
2X-RAY DIFFRACTION2chain 'A' and (resseq 8:18)
3X-RAY DIFFRACTION3chain 'A' and (resseq 19:25)
4X-RAY DIFFRACTION4chain 'A' and (resseq 26:32)
5X-RAY DIFFRACTION5chain 'A' and (resseq 33:39)
6X-RAY DIFFRACTION6chain 'A' and (resseq 40:48)
7X-RAY DIFFRACTION7chain 'A' and (resseq 49:90)
8X-RAY DIFFRACTION8chain 'A' and (resseq 91:101)
9X-RAY DIFFRACTION9chain 'A' and (resseq 102:107)

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