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- PDB-5jpj: Crystal structure of 6aJL2-R24G -

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Basic information

Entry
Database: PDB / ID: 5jpj
TitleCrystal structure of 6aJL2-R24G
Components6aJL2 protein
KeywordsIMMUNE SYSTEM / Amyloidosis / light chain / lambda
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPelaez-Aguilar, A.E. / Diaz-Vilchis, A. / Amero, C. / Becerril, B. / Rudino-Pinera, E.
Funding support Mexico, 1items
OrganizationGrant numberCountry
UNAMDGAPA IN 209114-3 Mexico
CitationJournal: Biochem Biophys Rep / Year: 2019
Title: Crystal structure of 6aJL2-R24G light chain variable domain: Does crystal packing explain amyloid fibril formation?
Authors: Rudino-Pinera, E. / Pelaez-Aguilar, A.E. / Amero, C. / Diaz-Vilchis, A.
History
DepositionMay 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 27, 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: 6aJL2 protein
B: 6aJL2 protein


Theoretical massNumber of molelcules
Total (without water)23,7242
Polymers23,7242
Non-polymers00
Water2,756153
1
A: 6aJL2 protein

A: 6aJL2 protein


Theoretical massNumber of molelcules
Total (without water)23,7242
Polymers23,7242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-x+1/2,y,-z1
Buried area1210 Å2
ΔGint-7 kcal/mol
Surface area10420 Å2
MethodPISA
2
B: 6aJL2 protein

B: 6aJL2 protein


Theoretical massNumber of molelcules
Total (without water)23,7242
Polymers23,7242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554x,-y,-z-1/21
Buried area1000 Å2
ΔGint-4 kcal/mol
Surface area10800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.929, 77.796, 93.387
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121

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Components

#1: Antibody 6aJL2 protein


Mass: 11861.768 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.68 Å3/Da / Density % sol: 54.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1 M sodium/potassium tartrate, 100 mM Tris-HCl, pH 7.0, 200 mM lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.18076 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 30, 2015
RadiationMonochromator: Si (111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18076 Å / Relative weight: 1
ReflectionResolution: 2→59.773 Å / Num. obs: 17490 / % possible obs: 98.7 % / Observed criterion σ(I): 2.3 / Redundancy: 4.6 % / Biso Wilson estimate: 31.48 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Net I/σ(I): 14.8
Reflection shellResolution: 2→2.001 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 2.3 / % possible all: 91.5

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2MKW

2mkw


Resolution: 2→46.694 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.6
RfactorNum. reflection% reflection
Rfree0.2488 900 5.18 %
Rwork0.1949 --
obs0.1976 17360 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 96.87 Å2 / Biso mean: 35.8515 Å2 / Biso min: 15.92 Å2
Refinement stepCycle: final / Resolution: 2→46.694 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1666 0 0 153 1819
Biso mean---41.07 -
Num. residues----222
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051808
X-RAY DIFFRACTIONf_angle_d0.7762480
X-RAY DIFFRACTIONf_chiral_restr0.049272
X-RAY DIFFRACTIONf_plane_restr0.004334
X-RAY DIFFRACTIONf_dihedral_angle_d14.7341094
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.12540.31231310.25752650X-RAY DIFFRACTION96
2.1254-2.28950.31811510.24112728X-RAY DIFFRACTION100
2.2895-2.51990.28631580.24182737X-RAY DIFFRACTION100
2.5199-2.88440.27071350.2232764X-RAY DIFFRACTION100
2.8844-3.63390.2471670.18672757X-RAY DIFFRACTION99
3.6339-100.20961580.15992824X-RAY DIFFRACTION97

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