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- PDB-3cdf: kI O18/O8 Y87H immunoglobulin light chain variable domain -

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Basic information

Entry
Database: PDB / ID: 3cdf
TitlekI O18/O8 Y87H immunoglobulin light chain variable domain
ComponentsIMMUNOGLOBULIN LIGHT CHAIN
KeywordsIMMUNE SYSTEM / Greek key beta barrel / amyloid / immunoglobulin / 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 / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsBaden, E.M. / Randles, E.G. / 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 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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
Revision 1.3Oct 30, 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

Downloads & links

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Assembly

Deposited unit
A: IMMUNOGLOBULIN LIGHT CHAIN
B: IMMUNOGLOBULIN LIGHT CHAIN
C: IMMUNOGLOBULIN LIGHT CHAIN
D: IMMUNOGLOBULIN LIGHT CHAIN
E: IMMUNOGLOBULIN LIGHT CHAIN
F: IMMUNOGLOBULIN LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)71,6776
Polymers71,6776
Non-polymers00
Water18,8441046
1
A: IMMUNOGLOBULIN LIGHT CHAIN
B: IMMUNOGLOBULIN LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)23,8922
Polymers23,8922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-9.3 kcal/mol
Surface area10240 Å2
MethodPISA
2
E: IMMUNOGLOBULIN LIGHT CHAIN
F: IMMUNOGLOBULIN LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)23,8922
Polymers23,8922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-10.6 kcal/mol
Surface area10210 Å2
MethodPISA
3
C: IMMUNOGLOBULIN LIGHT CHAIN

D: IMMUNOGLOBULIN LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)23,8922
Polymers23,8922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_454x-1,y,z-11
Buried area1430 Å2
ΔGint-10.5 kcal/mol
Surface area10240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.959, 98.043, 73.074
Angle α, β, γ (deg.)90.00, 119.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody
IMMUNOGLOBULIN LIGHT CHAIN


Mass: 11946.093 Da / Num. of mol.: 6 / Mutation: Y87H
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.: 1046 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCE OF THE PROTEIN WAS NOT AVAILABLE AT THE UNIPROT DATABASE (UNIPROT) AT THE TIME OF ...THE SEQUENCE OF THE PROTEIN WAS NOT AVAILABLE AT THE UNIPROT DATABASE (UNIPROT) AT THE TIME OF DEPOSITION.THE AUTHORS STATED MUTATIONS Y87H IN PROTEIN SEQUENCES

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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: 3.18 Å3/Da / Density % sol: 61.35 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.1
Details: 1.2 M sodium citrate in 0.1 M Tris buffer, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5241 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 11, 2007 / Details: Osmic Varimax
RadiationMonochromator: confocal optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5241 Å / Relative weight: 1
ReflectionResolution: 1.39→34.52 Å / Num. all: 177610 / Num. obs: 130900 / % possible obs: 73.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.31 % / Rsym value: 0.043 / Net I/σ(I): 14.5
Reflection shellResolution: 1.39→1.44 Å / Redundancy: 1.82 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.325 / % possible all: 13.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q20

2q20


Resolution: 1.53→17.56 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23147 2279 5 %RANDOM
Rwork0.18904 ---
obs0.19118 43135 99.93 %-
all-177610 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.79 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.53→17.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5536 0 0 1056 6592
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221862
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8581.962562
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.4945250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.94325.7580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.57815305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.25155
X-RAY DIFFRACTIONr_chiral_restr0.1550.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021477
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2160.2905
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.21340
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2408
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.247
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8061.51188
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.67821954
X-RAY DIFFRACTIONr_scbond_it3.5523674
X-RAY DIFFRACTIONr_scangle_it4.9884.5608
X-RAY DIFFRACTIONr_rigid_bond_restr1.65235993
X-RAY DIFFRACTIONr_sphericity_free7.3931055
X-RAY DIFFRACTIONr_sphericity_bonded4.82435536
LS refinement shellResolution: 1.53→1.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.517 167 -
Rwork0.507 3189 -
obs--99.79 %
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)
10.03690.0396-0.02440.369-0.05710.3167-0.00320.0040.00090.00420.005-0.00960.0064-0.0118-0.0017-0.0186-0.00080.0004-0.0144-0.0028-0.0289-35.332719.13382.8762
20.77360.11560.12040.07870.03670.19310.02520.0298-0.00840.0161-0.012-0.0021-0.0007-0.0065-0.0132-0.0133-0.0007-0.0014-0.02080.0024-0.0312-20.983234.2252-1.1271
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 108
2X-RAY DIFFRACTION2B-1 - 108

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