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- PDB-3u79: AL-103 Y32F Y96F -

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Basic information

Entry
Database: PDB / ID: 3u79
TitleAL-103 Y32F Y96F
ComponentsAmyloidogenic immunoglobulin light chain protein AL-103 Y32F Y96F, variable domain
KeywordsIMMUNE SYSTEM / immunoglobulin light chain variable domain
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.62 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. / F Volkman, B. / 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-103 Y32F Y96F, variable domain
B: Amyloidogenic immunoglobulin light chain protein AL-103 Y32F Y96F, variable domain
C: Amyloidogenic immunoglobulin light chain protein AL-103 Y32F Y96F, variable domain
D: Amyloidogenic immunoglobulin light chain protein AL-103 Y32F Y96F, variable domain
E: Amyloidogenic immunoglobulin light chain protein AL-103 Y32F Y96F, variable domain
F: Amyloidogenic immunoglobulin light chain protein AL-103 Y32F Y96F, variable domain
G: Amyloidogenic immunoglobulin light chain protein AL-103 Y32F Y96F, variable domain
H: Amyloidogenic immunoglobulin light chain protein AL-103 Y32F Y96F, variable domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,24934
Polymers97,4768
Non-polymers1,77326
Water22,3571241
1
A: Amyloidogenic immunoglobulin light chain protein AL-103 Y32F Y96F, variable domain
B: Amyloidogenic immunoglobulin light chain protein AL-103 Y32F Y96F, variable domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,93911
Polymers24,3692
Non-polymers5709
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12460 Å2
ΔGint-595 kcal/mol
Surface area38350 Å2
2
C: Amyloidogenic immunoglobulin light chain protein AL-103 Y32F Y96F, variable domain
G: Amyloidogenic immunoglobulin light chain protein AL-103 Y32F Y96F, variable domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7558
Polymers24,3692
Non-polymers3866
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Amyloidogenic immunoglobulin light chain protein AL-103 Y32F Y96F, variable domain
H: Amyloidogenic immunoglobulin light chain protein AL-103 Y32F Y96F, variable domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6837
Polymers24,3692
Non-polymers3145
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
E: Amyloidogenic immunoglobulin light chain protein AL-103 Y32F Y96F, variable domain
F: Amyloidogenic immunoglobulin light chain protein AL-103 Y32F Y96F, variable domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8728
Polymers24,3692
Non-polymers5036
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.020, 128.020, 98.840
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Antibody
Amyloidogenic immunoglobulin light chain protein AL-103 Y32F Y96F, variable domain


Mass: 12184.529 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1241 / 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: 2.4 Å3/Da / Density % sol: 48.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.21
Details: 20% (w/v) polyethylene glycol monomethyl ether and 0.2M Sodium Acetate in 0.1 M MES buffer (pH 8.21), VAPOR DIFFUSION, HANGING DROP, temperature 277K

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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: Apr 27, 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: 1.62→111 Å / Num. obs: 112286 / % possible obs: 95.4 % / Observed criterion σ(F): 4.89 / Observed criterion σ(I): 23.9
Reflection shellResolution: 1.62→1.69 Å / % possible all: 77.5

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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: 1.62→64.06 Å / SU ML: 0.48 / σ(F): 1.06 / Phase error: 23.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.223 1096 0.5 %
Rwork0.169 --
obs0.169 112286 95.5 %
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.91 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.1166 Å2-0 Å2-0 Å2
2--2.1166 Å2-0 Å2
3----4.2333 Å2
Refinement stepCycle: LAST / Resolution: 1.62→64.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6819 0 64 1241 8124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0257378
X-RAY DIFFRACTIONf_angle_d0.81410151
X-RAY DIFFRACTIONf_dihedral_angle_d13.9392722
X-RAY DIFFRACTIONf_chiral_restr0.0431108
X-RAY DIFFRACTIONf_plane_restr0.0021312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.69380.32781460.254228385X-RAY DIFFRACTION99
1.6938-1.78310.26331410.213328697X-RAY DIFFRACTION100
1.7831-1.89480.23811440.193928373X-RAY DIFFRACTION99
1.8948-2.04110.26861210.190623776X-RAY DIFFRACTION83
2.0411-2.24650.20291310.180827018X-RAY DIFFRACTION96
2.2465-2.57160.2061310.160926492X-RAY DIFFRACTION97
2.5716-3.23990.25771430.147528644X-RAY DIFFRACTION100
3.2399-64.060.18961390.157427432X-RAY DIFFRACTION96

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