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- PDB-2q20: Structure of the germline Vk1 O18/O8 light chain variable domain ... -

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Basic information

Entry
Database: PDB / ID: 2q20
TitleStructure of the germline Vk1 O18/O8 light chain variable domain homodimer
ComponentsVk1 O18/O8 germline light chain variable domain
KeywordsPROTEIN FIBRIL / Vk1 / germline / AL / light chain amyloidosis / amyloid / immunoglobulin / light chain / light chain variable domain
Function / homology
Function and homology information


CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex / 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 / Initial triggering of complement / immunoglobulin complex / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsThompson, J.R. / Ramirez-Alvarado, M. / Baden, E.M.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Altered dimer interface decreases stability in an amyloidogenic protein.
Authors: Baden, E.M. / Owen, B.A. / Peterson, F.C. / Volkman, B.F. / Ramirez-Alvarado, M. / Thompson, J.R.
History
DepositionMay 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Aug 30, 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 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999Sequence The sequence is not available in the UniProt database at the time of processing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vk1 O18/O8 germline light chain variable domain
B: Vk1 O18/O8 germline light chain variable domain


Theoretical massNumber of molelcules
Total (without water)23,9422
Polymers23,9422
Non-polymers00
Water8,179454
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.265, 74.265, 99.051
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Antibody Vk1 O18/O8 germline light chain variable domain


Mass: 11971.120 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Vk1 O18/O8 light chain germline / Plasmid: pET12a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold / References: UniProt: P01594
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / 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: 3.29 Å3/Da / Density % sol: 62.63 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: Protein: 890 micromolar in 10 mM TRIS pH 7.4. Mother Liquor: 15-30% (w/v) PEG 4K, 0.2 Li2SO4, 0.1 M TRIS pH 7.9-8.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.0718 Å
DetectorType: SBC-3 / Detector: CCD / Date: Feb 7, 2007 / Details: mirror
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0718 Å / Relative weight: 1
ReflectionResolution: 1.3→99 Å / Num. all: 74839 / Num. obs: 74839 / % possible obs: 99.7 % / Redundancy: 12.2 % / Biso Wilson estimate: 22.2 Å2 / Rsym value: 0.046 / Net I/σ(I): 53.2
Reflection shellResolution: 1.3→1.33 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 5311 / Rsym value: 0.53 / % possible all: 96.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: polyserine model of pdb entry 1BRE chain A

1bre


Resolution: 1.3→99 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.995 / SU ML: 0.019
Isotropic thermal model: Isotropic model later refinement cycles anisotropic
Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14815 535 0.7 %RANDOM
Rwork0.11935 ---
obs0.11955 74839 99.19 %-
all-74839 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.491 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20.03 Å20 Å2
2--0.06 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.3→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1970 0 0 454 2424
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222046
X-RAY DIFFRACTIONr_bond_other_d0.0030.021696
X-RAY DIFFRACTIONr_angle_refined_deg1.7731.9582837
X-RAY DIFFRACTIONr_angle_other_deg2.16434047
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4025287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.93226.19692
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.16315338
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.808155
X-RAY DIFFRACTIONr_chiral_restr0.1170.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022478
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02401
X-RAY DIFFRACTIONr_nbd_refined0.2650.2377
X-RAY DIFFRACTIONr_nbd_other0.2250.21769
X-RAY DIFFRACTIONr_nbtor_refined0.1930.21028
X-RAY DIFFRACTIONr_nbtor_other0.0910.21185
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3010.2388
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0620.22
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1320.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2320.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.252
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4591.51669
X-RAY DIFFRACTIONr_mcbond_other1.6821.5517
X-RAY DIFFRACTIONr_mcangle_it2.97722156
X-RAY DIFFRACTIONr_scbond_it4.53876
X-RAY DIFFRACTIONr_scangle_it5.5114.5678
X-RAY DIFFRACTIONr_rigid_bond_restr2.33334497
X-RAY DIFFRACTIONr_sphericity_free16.8213454
X-RAY DIFFRACTIONr_sphericity_bonded4.38833666
LS refinement shellResolution: 1.3→1.333 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 42 -
Rwork0.218 5311 -
obs-5311 96.28 %

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