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- PDB-3bdx: Crystal structure of the unstable and highly fibrillogenic Pro7Se... -

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Basic information

Entry
Database: PDB / ID: 3bdx
TitleCrystal structure of the unstable and highly fibrillogenic Pro7Ser mutant of the Recombinant variable domain 6AJL2
ComponentsAmyloid lambda 6 light chain variable region PIP (fragment)
KeywordsIMMUNE SYSTEM / Lambda VI subgroup / light chain variable domain / 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 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: 2.3 Å
AuthorsHernandez-Santoyo, A. / Fuentes-Silva, D. / Del Pozo Yauner, L. / Becerril, B. / Rodriguez-Romero, A.
CitationJournal: 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
DepositionNov 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999 SEQUENCE THE RESIDUES ARE NUMBERED CONSECUTIVELY IN THE POLYPEPTIDE CHAIN AND DO NOT FOLLOW THE ... SEQUENCE THE RESIDUES ARE NUMBERED CONSECUTIVELY IN THE POLYPEPTIDE CHAIN AND DO NOT FOLLOW THE KABAT NUMBERING SCHEME.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Amyloid lambda 6 light chain variable region PIP (fragment)
B: Amyloid lambda 6 light chain variable region PIP (fragment)
C: Amyloid lambda 6 light chain variable region PIP (fragment)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,71413
Polymers35,8563
Non-polymers85910
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Amyloid lambda 6 light chain variable region PIP (fragment)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3136
Polymers11,9521
Non-polymers3615
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Amyloid lambda 6 light chain variable region PIP (fragment)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2984
Polymers11,9521
Non-polymers3463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Amyloid lambda 6 light chain variable region PIP (fragment)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1033
Polymers11,9521
Non-polymers1512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.11, 106.12, 133.36
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-300-

HOH

21B-299-

HOH

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Components

#1: Antibody Amyloid lambda 6 light chain variable region PIP (fragment) / Recombinant light chain variable domain


Mass: 11951.873 Da / Num. of mol.: 3 / Fragment: Residues 1-111 / Mutation: P7S
Source method: isolated from a genetically manipulated source
Details: Promotor: lac Resistence ampicillin / Source: (gene. exp.) Homo sapiens (human) / Strain: Lambda VI light chain subgroup / 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
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


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


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.77 Å3/Da / Density % sol: 55.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Drops consisted of 5 microliters of protein solution (7 mg/mL) plus 5 microliters of 0.1 M MES pH 6.5, 2.0 M Sodium acetate trihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Sep 7, 2005 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→29.92 Å / Num. obs: 16902 / % possible obs: 93.9 % / Redundancy: 2.3 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 8.7
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 3.9 / Num. unique all: 2544

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3B5G

3b5g


Resolution: 2.3→29.92 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2014859.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1717 10.2 %RANDOM
Rwork0.205 ---
obs0.205 16809 92.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.4523 Å2 / ksol: 0.39712 e/Å3
Displacement parametersBiso mean: 22.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20 Å20 Å2
2--2.25 Å20 Å2
3----1.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2517 0 56 100 2673
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d26.8
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.111.5
X-RAY DIFFRACTIONc_mcangle_it1.822
X-RAY DIFFRACTIONc_scbond_it1.612
X-RAY DIFFRACTIONc_scangle_it2.212.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.313 317 11.1 %
Rwork0.264 2548 -
obs--97 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2act_xplor_par.txtact_xplor_top.txt
X-RAY DIFFRACTION3gol_xplor_par.txtgol_xplor_top.txt
X-RAY DIFFRACTION4mes_xplor_par.txtmes_xplor_top.txt
X-RAY DIFFRACTION5water_rep.paramwater.top

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