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- PDB-1hez: Structure of P. magnus protein L bound to a human IgM Fab. -

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Basic information

Entry
Database: PDB / ID: 1hez
TitleStructure of P. magnus protein L bound to a human IgM Fab.
Components
  • HEAVY CHAIN OF IG
  • KAPPA LIGHT CHAIN OF IG
  • PROTEIN L
KeywordsANTIBODY / SUPERANTIGEN
Function / homology
Function and homology information


hexameric IgM immunoglobulin complex / IgM B cell receptor complex / pentameric IgM immunoglobulin complex / IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / pre-B cell allelic exclusion / CD22 mediated BCR regulation / IgG immunoglobulin complex ...hexameric IgM immunoglobulin complex / IgM B cell receptor complex / pentameric IgM immunoglobulin complex / IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / pre-B cell allelic exclusion / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / IgG binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin binding / FCGR activation / immunoglobulin mediated immune response / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / complement activation, classical pathway / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / antigen binding / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antibacterial humoral response / defense response to Gram-negative bacterium / adaptive immune response / Potential therapeutics for SARS / blood microparticle / immune response / innate immune response / cell surface / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Protein G-related albumin-binding (GA) module / Extracellular matrix-binding protein ebh, GA module / GA module / GA module / Protein L, Ig light chain-binding / Protein L b1 domain / Repeat of unknown function DUF5633 / Family of unknown function (DUF5633) / Ubiquitin-like (UB roll) - #10 / GA-like domain ...Protein G-related albumin-binding (GA) module / Extracellular matrix-binding protein ebh, GA module / GA module / GA module / Protein L, Ig light chain-binding / Protein L b1 domain / Repeat of unknown function DUF5633 / Family of unknown function (DUF5633) / Ubiquitin-like (UB roll) - #10 / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Ubiquitin-like (UB roll) / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / Immunoglobulin kappa constant / Immunoglobulin heavy constant mu / Protein L
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
FINEGOLDIA MAGNA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGraille, M. / Stura, E.A. / Housden, N.G. / Bottomley, S.P. / Taussig, M.J. / Sutton, B.J. / Gore, M.G. / Charbonnier, J.B.
Citation
Journal: Structure / Year: 2001
Title: Complex between Peptostreptococcus Magnus Protein L and a Human Antibody Reveals Structural Convergence in the Interaction Modes of Fab Binding Modes
Authors: Graille, M. / Stura, E.A. / Housden, N.G. / Beckingham, J.A. / Bottomley, S.P. / Beale, D. / Taussig, M.J. / Sutton, B.J. / Gore, M.G. / Charbonnier, J.B.
#1: Journal: Biochem.J. / Year: 1999
Title: Interactions between a Single Immunoglobulin-Binding Domain of Protein L from Peptostreptococcus Magnus and a Human Kappa Light Chain
Authors: Beckingham, J.A. / Bottomley, S.P. / Hinton, R. / Sutton, B.J. / Gore, M.G.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Crystal Structure of a Staphylococcus Aureus Protein a Domain Complexed with the Fab Fragment of a Human Igm Antibody: Structural Basis for Recognition of B-Cell Receptors and Superantigen Activity
Authors: Graille, M. / Stura, E.A. / Corper, A.L. / Sutton, B.J. / Taussig, M.J. / Charbonnier, J.B. / Silverman, G.J.
#3: Journal: Bioseparation / Year: 1995
Title: Cloning, expression and purification of Ppl-1, a kappa-chain binding protein, based upon protein L from Peptostreptococcus magnus.
Authors: Bottomley, S.P. / Beckingham, J.A. / Murphy, J.P. / Atkinson, M. / Atkinson, T. / Hinton, R.J. / Gore, M.G.
History
DepositionNov 27, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.page_last / _citation.title
Revision 1.4Mar 17, 2021Group: Derived calculations / Other / Structure summary / Category: pdbx_database_status / struct / struct_site
Item: _pdbx_database_status.status_code_sf / _struct.title ..._pdbx_database_status.status_code_sf / _struct.title / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 13, 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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KAPPA LIGHT CHAIN OF IG
B: HEAVY CHAIN OF IG
C: KAPPA LIGHT CHAIN OF IG
D: HEAVY CHAIN OF IG
E: PROTEIN L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,2217
Polymers102,0835
Non-polymers1382
Water2,018112
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11780 Å2
ΔGint-69.6 kcal/mol
Surface area48480 Å2
MethodPQS
Unit cell
Length a, b, c (Å)55.185, 87.335, 210.538
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody KAPPA LIGHT CHAIN OF IG


Mass: 23373.871 Da / Num. of mol.: 2 / Fragment: 1-214 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell: B-LYMPHOCYTE / References: UniProt: P01834*PLUS
#2: Antibody HEAVY CHAIN OF IG


Mass: 24292.139 Da / Num. of mol.: 2 / Fragment: 501-724 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell: B-LYMPHOCYTE / References: UniProt: P01871*PLUS
#3: Protein PROTEIN L


Mass: 6750.485 Da / Num. of mol.: 1 / Fragment: 820-880 / Source method: isolated from a natural source / Source: (natural) FINEGOLDIA MAGNA (bacteria) / Plasmid: PKK223-3 / Strain: 3316 / References: UniProt: Q51918
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.13 Å3/Da / Density % sol: 63.1 %
Crystal growpH: 8.5
Details: 13-16% MPEG 5000, 100MM IMIDAZOLE MALATE, PH8.5, pH 8.50
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop / Details: used seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
113-16 %(w/w)mPEG50001reservoir
2100 mMimidazole malate1reservoir
35 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.962
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.962 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 26811 / % possible obs: 95.2 % / Redundancy: 4.66 % / Biso Wilson estimate: 59.53 Å2 / Rsym value: 0.112 / Net I/σ(I): 12.7
Reflection shellResolution: 2.7→2.78 Å / Redundancy: 5 % / Mean I/σ(I) obs: 2.9 / Rsym value: 0.374 / % possible all: 97.6
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / Rmerge(I) obs: 0.116
Reflection shell
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 2.68 Å / % possible obs: 93.7 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
CNS1refinement
HKLdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DEE

1dee


Resolution: 2.7→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 2
Details: SIDE CHAIN ATOMS FROM RESIDUES LYS A 45, LYS A 169, GLU B 89, LEU C 54, LYS C 107, GLU D 89, GLN D 113, GLU D 136, ARG D 181, LYS E 833 AND LYS E 878 ARE NOT DEFINED BY ELECTRONIC DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.278 1192 5 %RANDOM
Rwork0.215 ---
obs0.215 24298 84.5 %-
Solvent computationBsol: 22.3753 Å2 / ksol: 0.293557 e/Å3
Displacement parametersBiso mean: 45.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å / Luzzati d res low obs: 6 Å
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6936 0 10 112 7058
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0074
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.423
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.7→2.74 Å / Total num. of bins used: 23
RfactorNum. reflection% reflection
Rfree0.348 42 5 %
Rwork0.3132 819 -
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3IMIDAZOLE.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
LS refinement shell
*PLUS
Lowest resolution: 2.75 Å

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