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- PDB-1b0w: Structural comparison of amyloidogenic light chain dimer in two c... -

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Basic information

Entry
Database: PDB / ID: 1b0w
TitleStructural comparison of amyloidogenic light chain dimer in two crystal forms with nonamyloidogenic counterparts
ComponentsBENCE-JONES KAPPA I PROTEIN BRE
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN / AMYLOID
Function / homology
Function and homology information


CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / immunoglobulin complex / Initial triggering of complement / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / antigen binding ...CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / immunoglobulin complex / Initial triggering of complement / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / blood microparticle / adaptive immune response / Potential therapeutics for SARS / immune response / extracellular region / identical protein binding / plasma membrane
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 / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin kappa variable 1-33
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSchormann, N. / Benson, M.D.
Citation
Journal: Amyloid / Year: 1998
Title: Tertiary structures of amyloidogenic and non-amyloidogenic transthyretin variants: new model for amyloid fibril formation
Authors: Schormann, N. / Murrell, J.R. / Benson, M.D.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1995
Title: Tertiary Structure of an Amyloid Immunoglobulin Light Chain Protein: A Proposed Model for Amyloid Fibril Formation
Authors: Schormann, N. / Murrell, J.R. / Liepnieks, J.J. / Benson, M.D.
History
DepositionNov 13, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 16, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4May 30, 2018Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Data collection / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / struct_biol
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details ..._pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _struct_biol.details
Revision 1.5Aug 9, 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
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BENCE-JONES KAPPA I PROTEIN BRE
B: BENCE-JONES KAPPA I PROTEIN BRE
C: BENCE-JONES KAPPA I PROTEIN BRE


Theoretical massNumber of molelcules
Total (without water)35,8353
Polymers35,8353
Non-polymers00
Water1,874104
1
A: BENCE-JONES KAPPA I PROTEIN BRE


Theoretical massNumber of molelcules
Total (without water)11,9451
Polymers11,9451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BENCE-JONES KAPPA I PROTEIN BRE


Theoretical massNumber of molelcules
Total (without water)11,9451
Polymers11,9451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: BENCE-JONES KAPPA I PROTEIN BRE


Theoretical massNumber of molelcules
Total (without water)11,9451
Polymers11,9451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.040, 142.110, 77.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.49832, -0.86699, 0.00157), (0.86699, 0.49831, -0.00442), (0.00305, 0.00357, 0.99999)61.57912, 35.67698, 12.75636
2given(-0.4989, -0.86666, 0.00247), (0.86666, 0.4989, 0.00048), (-0.00082, -0.00238, 1)-61.69847, 35.61665, -12.67716
3given(-0.50279, 0.8644, 0.00444), (-0.8644, -0.5028, 0.00171), (0.00371, -0.00298, 0.99999)-61.54691, 106.75963, -25.65269
Detailsmonomer

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Components

#1: Antibody BENCE-JONES KAPPA I PROTEIN BRE / BENCE-JONES


Mass: 11945.124 Da / Num. of mol.: 3 / Fragment: VARIABLE DOMAIN OF LIGHT CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: PATIENT BRE / Plasmid: PCZ11
Gene (production host): CDNA (GENBANK ACCESSION CODE U31344)
Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: P01594
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.2 Å3/Da / Density % sol: 61.15 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: CRYSTALS OF BRE (20MG/ML IN 0.1M TRIS BUFFER, PH 7) WERE GROWN AT RT IN HANGING-DROPS USING 2.5M AMMONIUM SULFATE IN 0.1M CITRATE BUFFER (PH 5.5)., pH 6.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Feb 1, 1994 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→52.5 Å / Num. obs: 35142 / % possible obs: 76 % / Observed criterion σ(I): 1 / Redundancy: 2.3 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.047 / Net I/σ(I): 7.5
Reflection shellResolution: 1.75→2 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 1.92 / Rsym value: 0.255 / % possible all: 56

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Processing

Software
NameVersionClassification
bioteXdata collection
bioteXdata reduction
AMoREphasing
X-PLOR3.1refinement
bioteXdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BRE

1bre


Resolution: 1.8→5 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.299 1568 5 %RANDOM
Rwork0.226 ---
obs-31772 77.3 %-
Displacement parametersBiso mean: 25.3 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 1.8→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2520 0 0 104 2624
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.84
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.5
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.8→1.88 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.419 136 5.4 %
Rwork0.384 2535 -
obs--53.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3TOPH19.PEP

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