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- PDB-1qlr: CRYSTAL STRUCTURE OF THE FAB FRAGMENT OF A HUMAN MONOCLONAL IgM C... -

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Basic information

Entry
Database: PDB / ID: 1qlr
TitleCRYSTAL STRUCTURE OF THE FAB FRAGMENT OF A HUMAN MONOCLONAL IgM COLD AGGLUTININ
Components
  • IGM FAB REGION IV-J(H4)-C (KAU COLD AGGLUTININ)
  • IGM KAPPA CHAIN V-III (KAU COLD AGGLUTININ)
KeywordsIMMUNOGLOBULIN / AUTOANTIBODY / COLD AGGLUTININ / HUMAN IGM FAB FRAGMENT
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / : / IGK@ protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsCarvalho, J.G. / Cauerhff, A. / Goldbaum, F. / Leoni, J. / Polikarpov, I.
Citation
Journal: J Immunol. / Year: 2000
Title: Three-dimensional structure of the Fab from a human IgM cold agglutinin.
Authors: Cauerhff, A. / Braden, B.C. / Carvalho, J.G. / Aparicio, R. / Polikarpov, I. / Leoni, J. / Goldbaum, F.A.
#1: Journal: Protein Pept.Lett. / Year: 1998
Title: Crystallization and Preliminary Diffraction Studies of a Human Fabm with Anti-I Activity
Authors: Cauerhff, A. / Polikarpov, I. / Mathov, I. / Abatangelo, C. / Plotkin, L. / Goldbaum, F.A. / Leoni, J.
#2: Journal: J.Biol.Chem. / Year: 1991
Title: The Primary Structure of the Fab Fragment of Protein Kau, a Monoclonal Immunoglobulin M Cold Agglutinin
Authors: Leoni, J. / Ghiso, J. / Goni, F. / Frangione, B.
History
DepositionSep 11, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp / citation ...chem_comp / citation / citation_author / pdbx_database_status / struct_conn
Item: _chem_comp.type / _citation.journal_abbrev ..._chem_comp.type / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _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.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_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 11, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Dec 13, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Oct 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

Downloads & links

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Assembly

Deposited unit
A: IGM KAPPA CHAIN V-III (KAU COLD AGGLUTININ)
B: IGM FAB REGION IV-J(H4)-C (KAU COLD AGGLUTININ)
C: IGM KAPPA CHAIN V-III (KAU COLD AGGLUTININ)
D: IGM FAB REGION IV-J(H4)-C (KAU COLD AGGLUTININ)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,7206
Polymers96,9864
Non-polymers7352
Water00
1
A: IGM KAPPA CHAIN V-III (KAU COLD AGGLUTININ)
B: IGM FAB REGION IV-J(H4)-C (KAU COLD AGGLUTININ)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8603
Polymers48,4932
Non-polymers3671
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: IGM KAPPA CHAIN V-III (KAU COLD AGGLUTININ)
D: IGM FAB REGION IV-J(H4)-C (KAU COLD AGGLUTININ)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8603
Polymers48,4932
Non-polymers3671
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.660, 115.660, 174.950
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.4815, 0.8763, 0.0152), (0.8759, -0.4806, -0.0428), (-0.0302, 0.0339, -0.999)-60.117, 101.9889, 141.5782
2given(0.4813, 0.876, 0.0329), (0.8764, -0.4802, -0.0365), (-0.0162, 0.0464, -0.9988)-62.0757, 101.3965, 140.93381

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Components

#1: Antibody IGM KAPPA CHAIN V-III (KAU COLD AGGLUTININ)


Mass: 23301.770 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source
Details: FAB FRAGMENT WAS PREPARED BY DIGESTION OF MONOCLONAL IGM KAU PURIFIED FROM PATIENT WITH AIHA.
Source: (natural) HOMO SAPIENS (human) / Cell: B-LYMPHOCYTE / Cellular location: EXTRACELLULAR / References: PIR: A23746, UniProt: Q6PJF2*PLUS
#2: Antibody IGM FAB REGION IV-J(H4)-C (KAU COLD AGGLUTININ)


Mass: 25191.094 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source
Details: FAB FRAGMENT WAS PREPARED BY DIGESTION OF MONOCLONAL IGM KAU PURIFIED FROM PATIENT WITH AIHA.
Source: (natural) HOMO SAPIENS (human) / Cell: B-LYMPHOCYTE / Cellular location: EXTRACELLULAR / References: PIR: B23746
#3: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
Has protein modificationY
Sequence detailsTHE SEQUENCE IS DESCRIBED IN J.LEONI,J.GHISO,F.GONI,B.FRANGIONE, J.BIOL.CHEM. 1991 V.266 2836-42 ...THE SEQUENCE IS DESCRIBED IN J.LEONI,J.GHISO,F.GONI,B.FRANGIONE, J.BIOL.CHEM. 1991 V.266 2836-42 THE CYS TO GLY CONFLICTS DETAILED IN SEQADV ARE DIFFERENCES BETWEEN THE PIR AND THE ELECTRON DENSITY. THE OBSERVED CYS RESIDUES ARE CHARACTERISTIC OF THE FAB IMMUNOGLOBULIN FOLD

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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: 3.38 Å3/Da / Density % sol: 64 %
Crystal growpH: 7.5 / Details: 14%(W/W) PEG 8000, 0.1 M SODIUM HEPES PH 7.5
Crystal grow
*PLUS
Temperature: 25 ℃ / Method: vapor diffusion, hanging drop / Details: Cauerhff, A., (1998) Protein Pept.Lett., 5, 177.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
214 %(w/w)PEG80001reservoir
30.1 Msodium HEPES1reservoir

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.38
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 1998 / Details: BENT MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.38 Å / Relative weight: 1
ReflectionResolution: 2.83→13.1 Å / Num. obs: 31329 / % possible obs: 96.8 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Rmerge(I) obs: 0.069 / Rsym value: 0.069
Reflection shellResolution: 2.83→2.89 Å / % possible all: 95.4
Reflection shell
*PLUS
% possible obs: 99 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DFB

1dfb


Resolution: 2.83→13.1 Å / SU B: 12.46 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.84 / ESU R Free: 0.36
Details: RESIDUES B,D 135 - 143, B,D 195 - 201, B,D 226 - 232, WERE NOT MODELED DUE TO LACK OF ELETRONIC DENSIT MAP. THE CONFORMATION OF RESIDUES B,D 202 - 204 SHOULD BE CONSIDERED AS A TENTATIVE.
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1578 5 %RANDOM
Rwork0.216 ---
obs-31329 96.8 %-
Displacement parametersBiso mean: 43.6 Å2
Refinement stepCycle: LAST / Resolution: 2.83→13.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6492 0 48 0 6540
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0470.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.050.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.752
X-RAY DIFFRACTIONp_mcangle_it3.063
X-RAY DIFFRACTIONp_scbond_it1.892
X-RAY DIFFRACTIONp_scangle_it3.113
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.77
X-RAY DIFFRACTIONp_staggered_tor21.115
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.216
Solvent computation
*PLUS
Displacement parameters
*PLUS

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