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- PDB-5c9k: Crystal structure of a highly fibrillogenic Arg24Gly mutant of th... -

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Basic information

Entry
Database: PDB / ID: 5c9k
TitleCrystal structure of a highly fibrillogenic Arg24Gly mutant of the Recombinant variable domain 6AJL2
ComponentsAmyloid lambda 6 light chain variable region PIP
KeywordsIMMUNE SYSTEM / LAMBDA VI SUBGROUP / BETA-SANDWICH / IMMUNOGLOBULIN / AL AMYLOIDOSIS
Function / homology
Function and homology information


immune response / extracellular space
Similarity search - Function
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
ACETATE ION / Amyloid lambda 6 light chain variable region PIP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsHernandez-Santoyo, A. / Rodriguez-Romero, A. / Luna-Martinez, O.D. / Becerril-Lujan, B.
Citation
#1: Journal: J. Mol. Biol. / Year: 2010
Title: A single mutation at the sheet switch region results in conformational changes favoring lambda6 light-chain fibrillogenesis.
Authors: Hernandez-Santoyo, A. / del Pozo Yauner, L. / Fuentes-Silva, D. / Ortiz, E. / Rudino-Pinera, E. / Sanchez-Lopez, R. / Horjales, E. / Becerril, B. / Rodriguez-Romero, A.
History
DepositionJun 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amyloid lambda 6 light chain variable region PIP
B: Amyloid lambda 6 light chain variable region PIP
C: Amyloid lambda 6 light chain variable region PIP
D: Amyloid lambda 6 light chain variable region PIP
E: Amyloid lambda 6 light chain variable region PIP
F: Amyloid lambda 6 light chain variable region PIP
G: Amyloid lambda 6 light chain variable region PIP
H: Amyloid lambda 6 light chain variable region PIP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,13012
Polymers94,8948
Non-polymers2364
Water18,1951010
1
A: Amyloid lambda 6 light chain variable region PIP


Theoretical massNumber of molelcules
Total (without water)11,8621
Polymers11,8621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Amyloid lambda 6 light chain variable region PIP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9803
Polymers11,8621
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Amyloid lambda 6 light chain variable region PIP


Theoretical massNumber of molelcules
Total (without water)11,8621
Polymers11,8621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Amyloid lambda 6 light chain variable region PIP


Theoretical massNumber of molelcules
Total (without water)11,8621
Polymers11,8621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Amyloid lambda 6 light chain variable region PIP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9212
Polymers11,8621
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Amyloid lambda 6 light chain variable region PIP


Theoretical massNumber of molelcules
Total (without water)11,8621
Polymers11,8621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Amyloid lambda 6 light chain variable region PIP


Theoretical massNumber of molelcules
Total (without water)11,8621
Polymers11,8621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Amyloid lambda 6 light chain variable region PIP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9212
Polymers11,8621
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
A: Amyloid lambda 6 light chain variable region PIP
G: Amyloid lambda 6 light chain variable region PIP


Theoretical massNumber of molelcules
Total (without water)23,7242
Polymers23,7242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-7 kcal/mol
Surface area10480 Å2
MethodPISA
10
B: Amyloid lambda 6 light chain variable region PIP
hetero molecules

H: Amyloid lambda 6 light chain variable region PIP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9015
Polymers23,7242
Non-polymers1773
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area1450 Å2
ΔGint-9 kcal/mol
Surface area10570 Å2
MethodPISA
11
C: Amyloid lambda 6 light chain variable region PIP
E: Amyloid lambda 6 light chain variable region PIP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7833
Polymers23,7242
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-9 kcal/mol
Surface area10450 Å2
MethodPISA
12
D: Amyloid lambda 6 light chain variable region PIP
F: Amyloid lambda 6 light chain variable region PIP


Theoretical massNumber of molelcules
Total (without water)23,7242
Polymers23,7242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-6 kcal/mol
Surface area10380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.556, 95.633, 102.583
Angle α, β, γ (deg.)90.00, 96.00, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-280-

HOH

21G-280-

HOH

31H-400-

HOH

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Components

#1: Antibody
Amyloid lambda 6 light chain variable region PIP


Mass: 11861.768 Da / Num. of mol.: 8 / Mutation: R24G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VL GENE SEGMENT 6A AND JL2/3 GENE SEGMENT / Plasmid: PSYN1 / Production host: Escherichia coli (E. coli) / Strain (production host): W3110 / References: UniProt: Q96JD1*PLUS
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1010 / 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: 2.69 Å3/Da / Density % sol: 54.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: SOLUTION 7 FROM CRYSTAL REMARK 280 SCREEN I (HAMPTON RESEARCH), PH 6.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 291K

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.92→34.7 Å / Num. all: 76561 / Num. obs: 76561 / % possible obs: 100 % / Redundancy: 2.9 % / Biso Wilson estimate: 19.56 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 13.1
Reflection shellResolution: 1.92→2 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10pre_2083: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3B5G

3b5g


Resolution: 1.92→34.646 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.219 3800 4.97 %Random selection
Rwork0.17 ---
obs0.1725 76511 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23 Å2
Refinement stepCycle: LAST / Resolution: 1.92→34.646 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6650 0 16 1010 7676
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116840
X-RAY DIFFRACTIONf_angle_d1.2659324
X-RAY DIFFRACTIONf_dihedral_angle_d14.5754084
X-RAY DIFFRACTIONf_chiral_restr0.0561037
X-RAY DIFFRACTIONf_plane_restr0.0061230
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.94430.3811340.30082668X-RAY DIFFRACTION100
1.9443-1.96990.33521360.27342722X-RAY DIFFRACTION100
1.9699-1.99690.29991310.24572643X-RAY DIFFRACTION100
1.9969-2.02540.26921510.22372727X-RAY DIFFRACTION100
2.0254-2.05560.2671350.21332651X-RAY DIFFRACTION100
2.0556-2.08770.27571440.19492698X-RAY DIFFRACTION100
2.0877-2.1220.27271530.20252638X-RAY DIFFRACTION100
2.122-2.15850.25931100.19862737X-RAY DIFFRACTION100
2.1585-2.19780.24261590.18962647X-RAY DIFFRACTION100
2.1978-2.24010.26621440.18742686X-RAY DIFFRACTION100
2.2401-2.28580.25741310.18942749X-RAY DIFFRACTION100
2.2858-2.33550.25241500.17962649X-RAY DIFFRACTION100
2.3355-2.38980.2451360.17612689X-RAY DIFFRACTION100
2.3898-2.44950.24831350.16822720X-RAY DIFFRACTION100
2.4495-2.51570.23141320.17152676X-RAY DIFFRACTION100
2.5157-2.58970.24581560.16032661X-RAY DIFFRACTION100
2.5897-2.67330.25131320.17072705X-RAY DIFFRACTION100
2.6733-2.76880.21361190.16562708X-RAY DIFFRACTION100
2.7688-2.87960.26921220.17042706X-RAY DIFFRACTION100
2.8796-3.01060.2051440.16542707X-RAY DIFFRACTION100
3.0106-3.16920.22241290.15962712X-RAY DIFFRACTION100
3.1692-3.36760.19231430.15362710X-RAY DIFFRACTION100
3.3676-3.62740.19031460.15112685X-RAY DIFFRACTION100
3.6274-3.9920.18581570.14622703X-RAY DIFFRACTION100
3.992-4.56850.13441480.12252702X-RAY DIFFRACTION100
4.5685-5.75150.15681570.13662710X-RAY DIFFRACTION100
5.7515-34.65130.22651660.18632702X-RAY DIFFRACTION98

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