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- PDB-1pew: High Resolution Crystal Structure of Jto2, a mutant of the non-am... -

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Entry
Database: PDB / ID: 1pew
TitleHigh Resolution Crystal Structure of Jto2, a mutant of the non-amyloidogenic Lamba6 Light Chain, Jto
ComponentsJto2, a LAMBDA-6 TYPE IMMUNOGLOBULIN LIGHT CHAIN, VARIABLE DOMAIN
KeywordsIMMUNE SYSTEM / Beta Sheet
Function / homology
Function and homology information


CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / immunoglobulin complex / 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 / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / immunoglobulin complex / 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 / Potential therapeutics for SARS / adaptive immune response / immune response / extracellular region / 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 lambda variable 6-57 / Immunoglobulin lambda variable 6-57
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDealwis, C. / Gupta, V. / Wilkerson, M.
CitationJournal: J.Mol.Recog. / Year: 2004
Title: Structural basis of light chain amyloidogenicity: comparison of the thermodynamic properties, fibrillogenic potential and tertiary structural features of four V(lambda)6 proteins
Authors: Wall, J.S. / Gupta, V. / Wilkerson, M. / Schell, M. / Loris, R. / Adams, P. / Solomon, A. / Stevens, F. / Dealwis, C.
History
DepositionMay 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / Version format compliance
Revision 1.3Aug 16, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Jto2, a LAMBDA-6 TYPE IMMUNOGLOBULIN LIGHT CHAIN, VARIABLE DOMAIN
B: Jto2, a LAMBDA-6 TYPE IMMUNOGLOBULIN LIGHT CHAIN, VARIABLE DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2486
Polymers23,7982
Non-polymers4504
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Jto2, a LAMBDA-6 TYPE IMMUNOGLOBULIN LIGHT CHAIN, VARIABLE DOMAIN
B: Jto2, a LAMBDA-6 TYPE IMMUNOGLOBULIN LIGHT CHAIN, VARIABLE DOMAIN
hetero molecules

A: Jto2, a LAMBDA-6 TYPE IMMUNOGLOBULIN LIGHT CHAIN, VARIABLE DOMAIN
B: Jto2, a LAMBDA-6 TYPE IMMUNOGLOBULIN LIGHT CHAIN, VARIABLE DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,49512
Polymers47,5964
Non-polymers8998
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554-x,y,-z-11
Buried area5200 Å2
ΔGint-72 kcal/mol
Surface area19390 Å2
MethodPISA, PQS
3
B: Jto2, a LAMBDA-6 TYPE IMMUNOGLOBULIN LIGHT CHAIN, VARIABLE DOMAIN
hetero molecules

B: Jto2, a LAMBDA-6 TYPE IMMUNOGLOBULIN LIGHT CHAIN, VARIABLE DOMAIN
hetero molecules

A: Jto2, a LAMBDA-6 TYPE IMMUNOGLOBULIN LIGHT CHAIN, VARIABLE DOMAIN
hetero molecules

A: Jto2, a LAMBDA-6 TYPE IMMUNOGLOBULIN LIGHT CHAIN, VARIABLE DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,49512
Polymers47,5964
Non-polymers8998
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_524x,-y-3,-z-1/21
crystal symmetry operation2_525-x,-y-3,z+1/21
crystal symmetry operation5_554-x,y,-z-11
Buried area3780 Å2
ΔGint-59 kcal/mol
Surface area20810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.577, 73.577, 92.298
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Cell settingtetragonal
Space group name H-MP4122

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Components

#1: Antibody Jto2, a LAMBDA-6 TYPE IMMUNOGLOBULIN LIGHT CHAIN, VARIABLE DOMAIN / immunoglobulin lambda light chain VLJ region


Mass: 11898.972 Da / Num. of mol.: 2 / Fragment: IMMUNOGLOBULIN LIGHT CHAIN, VARIABLE DOMAIN / Mutation: D29A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Jto / Plasmid: pET-27b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21DE3 / References: UniProt: P06317, UniProt: P01721*PLUS
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.54 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1M Na Acetate, 0.8M Amm. Sulfate, 100mM Cadmium chloride, 10% n-Decyl-B-D-maltoside, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.5418 Å
DetectorType: RIGAKU AFC-5R / Detector: DIFFRACTOMETER / Date: Sep 15, 2001
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→15 Å / Num. all: 32368 / Num. obs: 31495 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 13.3 % / Rsym value: 0.066 / Net I/σ(I): 20.2
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 5.4 / Num. unique all: 3339 / Rsym value: 0.515 / % possible all: 93.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CD0

1cd0


Resolution: 1.6→8 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.907 / SU B: 3.385 / SU ML: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 4 / ESU R: 0.125 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27291 1633 4.9 %RANDOM
Rwork0.2522 ---
all0.295 ---
obs0.2533 31495 97.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.751 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2--0.14 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1647 0 4 104 1755
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211687
X-RAY DIFFRACTIONr_angle_refined_deg1.291.9392288
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9625212
X-RAY DIFFRACTIONr_chiral_restr0.0820.2251
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021318
X-RAY DIFFRACTIONr_nbd_refined0.2280.2777
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.23
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2340.2139
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3340.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3520.211
X-RAY DIFFRACTIONr_mcbond_it0.531.51070
X-RAY DIFFRACTIONr_mcangle_it0.90421727
X-RAY DIFFRACTIONr_scbond_it1.5653617
X-RAY DIFFRACTIONr_scangle_it2.2344.5561
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.371 109
Rwork0.356 2114
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)
14.40540.0468-0.22153.30520.63533.7139-0.172-0.2481-0.25590.0664-0.04740.09790.11940.04040.21940.1128-0.00180.01690.00110.00850.078111.9083-100.4335-60.9006
28.3907-0.0137-4.75092.8506-0.92836.37370.81330.80940.77870.2501-0.09720.2009-0.951-0.8149-0.71610.24950.19530.11790.26270.15440.16868.0555-117.2196-37.5231
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 108
2X-RAY DIFFRACTION2B1 - 108

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