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- PDB-4aj0: Crystallographic structure of an amyloidogenic variant, 3rCW, of ... -

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Basic information

Entry
Database: PDB / ID: 4aj0
TitleCrystallographic structure of an amyloidogenic variant, 3rCW, of the germinal line lambda 3
ComponentsGERMINAL LINE LAMBDA 3 3RCW VARIANT
KeywordsIMMUNE SYSTEM / AMYLOIDOSIS
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION
Function and homology information
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsVillalba, M.I. / Luna, O.D. / Rudino-Pinera, E. / Sanchez, R. / Sanchez-Lopez, R. / Rojas-Trejo, S. / Olamendi-Portugal, T. / Fernandez-Velasco, D.A. / Becerril, B.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Site-Directed Mutagenesis Reveals Regions Implicated in the Stability and Fiber Formation of Human Lambda3R Light Chains.
Authors: Villalba, M.I. / Canul-Tec, J.C. / Luna-Martinez, O.D. / Sanchez-Alcala, R. / Olamendi-Portugal, T. / Rudino-Pinera, E. / Rojas, S. / Sanchez-Lopez, R. / Fernandez-Velasco, D.A. / Becerril, B.
History
DepositionFeb 15, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Feb 11, 2015Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GERMINAL LINE LAMBDA 3 3RCW VARIANT
B: GERMINAL LINE LAMBDA 3 3RCW VARIANT
C: GERMINAL LINE LAMBDA 3 3RCW VARIANT
D: GERMINAL LINE LAMBDA 3 3RCW VARIANT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4537
Polymers45,1534
Non-polymers2993
Water6,575365
1
A: GERMINAL LINE LAMBDA 3 3RCW VARIANT
C: GERMINAL LINE LAMBDA 3 3RCW VARIANT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8765
Polymers22,5772
Non-polymers2993
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-13.9 kcal/mol
Surface area13160 Å2
MethodPISA
2
B: GERMINAL LINE LAMBDA 3 3RCW VARIANT
D: GERMINAL LINE LAMBDA 3 3RCW VARIANT


Theoretical massNumber of molelcules
Total (without water)22,5772
Polymers22,5772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-5 kcal/mol
Surface area13010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.807, 41.807, 171.035
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Antibody
GERMINAL LINE LAMBDA 3 3RCW VARIANT


Mass: 11288.354 Da / Num. of mol.: 4 / Fragment: VARIABLE DOMAIN VARIANT OF 3RJL2, RESIDUES 1-107
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: precipitant*YM
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsBECAUSE THIS VARIANT IS RESULT OF MODIFICATIONS OVER 3RJL2 IT IS NOT DEPOSITED IN ANY DATA BASE. ...BECAUSE THIS VARIANT IS RESULT OF MODIFICATIONS OVER 3RJL2 IT IS NOT DEPOSITED IN ANY DATA BASE. CONTAINS MUTATIONS C34Y, W91A.

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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: 1.85 Å3/Da / Density % sol: 33.65 % / Description: NONE
Crystal growpH: 3 / Details: 1.6 M AMMONIUM SULFATE, 40 % TREHALOSE, pH 3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.972
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 1, 2011
Details: DOUBLE CRYSTAL CHANNEL CUT, SI(111), 1M LONG RH COATED TOROIDAL MIRROR FOR VERTICAL AND HORIZONTAL FOCUSING.
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 36831 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 18.46 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.2
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.8 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LIL

1lil


Resolution: 1.7→27.631 Å / SU ML: 0.47 / σ(F): 2.02 / Phase error: 21.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2116 1835 5 %
Rwork0.1741 --
obs0.1765 36764 99.95 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.599 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso mean: 23.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.0792 Å20 Å20 Å2
2---0.0792 Å20 Å2
3---0.1583 Å2
Refinement stepCycle: LAST / Resolution: 1.7→27.631 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3150 0 16 365 3531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063636
X-RAY DIFFRACTIONf_angle_d1.1355008
X-RAY DIFFRACTIONf_dihedral_angle_d13.8331335
X-RAY DIFFRACTIONf_chiral_restr0.084548
X-RAY DIFFRACTIONf_plane_restr0.005684
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7001-1.74610.28761210.25772720X-RAY DIFFRACTION100
1.7461-1.79740.31051420.22822671X-RAY DIFFRACTION100
1.7974-1.85540.26161450.21122649X-RAY DIFFRACTION100
1.8554-1.92170.27461460.1932695X-RAY DIFFRACTION100
1.9217-1.99870.23971530.17732724X-RAY DIFFRACTION100
1.9987-2.08960.21851410.16662701X-RAY DIFFRACTION100
2.0896-2.19970.23291280.16592694X-RAY DIFFRACTION100
2.1997-2.33750.22611390.17832670X-RAY DIFFRACTION100
2.3375-2.51780.26241300.18882681X-RAY DIFFRACTION100
2.5178-2.7710.28551340.18212706X-RAY DIFFRACTION100
2.771-3.17150.20721480.17672676X-RAY DIFFRACTION100
3.1715-3.99380.19641630.15342657X-RAY DIFFRACTION100
3.9938-27.63460.16661450.15532685X-RAY DIFFRACTION100

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