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- PDB-3b5g: Crystal Structure of the Unstable and Highly Fibrillogenic PRO7SE... -

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Basic information

Entry
Database: PDB / ID: 3b5g
TitleCrystal Structure of the Unstable and Highly Fibrillogenic PRO7SER Mutant of the Recombinant Variable Domain 6AJL2
ComponentsAMYLOID LAMBDA 6 LIGHT CHAIN VARIABLE REGION PIP
KeywordsIMMUNE SYSTEM / Lambda VI subgroup / light chain variable domain / beta-sandwich / immunoglobulin / AL 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: 1.9 Å
AuthorsHernandez-Santoyo, A. / 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
DepositionOct 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,68912
Polymers23,9042
Non-polymers78610
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.770, 68.590, 83.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody AMYLOID LAMBDA 6 LIGHT CHAIN VARIABLE REGION PIP


Mass: 11951.873 Da / Num. of mol.: 2 / Fragment: residues 1-111 / Mutation: P7S
Source method: isolated from a genetically manipulated source
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
#2: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE RESIDUES ARE NUMBERED CONSECUTIVELY IN THE POLYPEPTIDE CHAIN AND DO NOT FOLLOW THE KABAT.

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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: 2.45 Å3/Da / Density % sol: 49.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Drops consisted of 5 microL of protein solution (7 mg/mL) plus 5 microL of Solution 7 from Crystal Screen I (Hampton Research), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.9→53 Å / Num. all: 19189 / Num. obs: 19208 / % possible obs: 99.9 % / Redundancy: 11.6 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 21.4
Reflection shellResolution: 1.9→1.949 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 6.1 / Num. unique all: 1228 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2CD0

2cd0


Resolution: 1.9→32.34 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.648 / SU ML: 0.084 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1957 10.2 %RANDOM
Rwork0.164 ---
obs0.168 17185 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.235 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→32.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1678 0 51 161 1890
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.013
X-RAY DIFFRACTIONr_angle_refined_deg1.436
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.715
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.27
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.064
X-RAY DIFFRACTIONr_chiral_restr0.1
X-RAY DIFFRACTIONr_gen_planes_refined
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 142 -
Rwork0.197 1228 -
obs--98.7 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.77250.094-0.62182.3196-0.54160.8008-0.0039-0.10060.0093-0.1148-0.0093-0.1030.09370.03260.0132-0.0170.00740.0032-0.0345-0.0081-0.069431.607523.664856.1857
20.78310.1709-0.43091.1699-0.12190.79050.03110.01970.0205-0.05290.0330.0213-0.0194-0.028-0.0641-0.02350.00270.0102-0.01470.0083-0.029816.205839.57250.9578
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1111 - 111
2X-RAY DIFFRACTION2BB1 - 1111 - 111

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