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- PDB-3cdy: AL-09 H87Y, immunoglobulin light chain variable domain -

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Basic information

Entry
Database: PDB / ID: 3cdy
TitleAL-09 H87Y, immunoglobulin light chain variable domain
ComponentsIMMUNOGLOBULIN LIGHT CHAIN
KeywordsIMMUNE SYSTEM / Greek key beta barrel / immunoglobulin / light chain / variable domain / amyloidosis
Function / homology
Function and homology information


CD22 mediated BCR regulation / immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / FCERI mediated Ca+2 mobilization ...CD22 mediated BCR regulation / immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / 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 / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / antigen binding / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / adaptive immune response / Potential therapeutics for SARS / blood microparticle / immune response / extracellular space / 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 / Immunoglobulins / 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 / Immunoglobulins / Immunoglobulin-like fold / 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: 2.43 Å
AuthorsBaden, E.M. / Randles, E.G. / Aboagye, A.K. / Thompson, J.R. / Ramirez-Alvarado, M.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structural insights into the role of mutations in amyloidogenesis.
Authors: Baden, E.M. / Randles, E.G. / Aboagye, A.K. / Thompson, J.R. / Ramirez-Alvarado, M.
History
DepositionFeb 27, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: IMMUNOGLOBULIN LIGHT CHAIN
B: IMMUNOGLOBULIN LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)23,9942
Polymers23,9942
Non-polymers00
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-10.8 kcal/mol
Surface area9920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.971, 73.971, 95.070
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 IMMUNOGLOBULIN LIGHT CHAIN


Mass: 11997.176 Da / Num. of mol.: 2 / Mutation: H87Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: kI O18/O8 germline / Plasmid: pET12a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Gold / References: UniProt: P01594*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 3.15 Å3/Da / Density % sol: 60.98 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 30% w/v polyethylene glycol 4000 and 0.2 M Li2SO4 in 0.1 M Tris buffer, pH 8.3, 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: 0.979508 Å
DetectorType: SBC-3 / Detector: CCD / Date: Jul 1, 2007 / Details: Si monochromator
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979508 Å / Relative weight: 1
ReflectionResolution: 2.43→64.061 Å / Num. all: 11200 / Num. obs: 10539 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Biso Wilson estimate: 57.129 Å2 / Rsym value: 0.101 / Net I/σ(I): 39.38
Reflection shellResolution: 2.43→2.52 Å / Redundancy: 10.4 % / Mean I/σ(I) obs: 7.86 / Num. unique all: 1029 / Rsym value: 0.365 / % possible all: 91.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q20

2q20


Resolution: 2.43→64.02 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.918 / SU B: 19.941 / SU ML: 0.235 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.413 / ESU R Free: 0.29 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26265 494 4.9 %RANDOM
Rwork0.18927 ---
all0.19293 10622 --
obs0.19293 9593 90.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.712 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20.26 Å20 Å2
2--0.51 Å20 Å2
3----0.77 Å2
Refinement stepCycle: LAST / Resolution: 2.43→64.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1676 0 0 88 1764
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221737
X-RAY DIFFRACTIONr_bond_other_d0.0010.021482
X-RAY DIFFRACTIONr_angle_refined_deg1.7891.9642371
X-RAY DIFFRACTIONr_angle_other_deg0.91333491
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7395220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.35125.58477
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.26115281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.555155
X-RAY DIFFRACTIONr_chiral_restr0.1040.2265
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021958
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02333
X-RAY DIFFRACTIONr_nbd_refined0.1950.2276
X-RAY DIFFRACTIONr_nbd_other0.1970.21507
X-RAY DIFFRACTIONr_nbtor_refined0.1880.2791
X-RAY DIFFRACTIONr_nbtor_other0.0910.21079
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.276
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2070.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4040.212
X-RAY DIFFRACTIONr_mcbond_it0.871.51396
X-RAY DIFFRACTIONr_mcbond_other0.1571.5445
X-RAY DIFFRACTIONr_mcangle_it1.16921776
X-RAY DIFFRACTIONr_scbond_it1.8763774
X-RAY DIFFRACTIONr_scangle_it2.774.5594
LS refinement shellResolution: 2.43→2.494 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 30 -
Rwork0.269 706 -
obs--89.21 %
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)
14.20371.51151.21882.1538-0.41284.8424-0.0909-0.21170.0154-0.02910.15450.0689-0.0828-0.8563-0.0635-0.2116-0.02630.01360.053-0.0045-0.136318.6134-28.735412.8864
23.96990.68341.59841.2855-0.39376.1755-0.2520.4714-0.01270.04740.0369-0.0814-0.4640.87720.2152-0.1567-0.0861-0.0013-0.01040.0272-0.119839.3192-23.49289.5126
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 1072 - 109
2X-RAY DIFFRACTION2BB0 - 1072 - 109

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