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- PDB-2mpa: BACTERICIDAL ANTIBODY AGAINST NEISSERIA MENINGITIDIS -

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Basic information

Entry
Database: PDB / ID: 2mpa
TitleBACTERICIDAL ANTIBODY AGAINST NEISSERIA MENINGITIDIS
Components
  • CONJUGATE OF PORA P1.16 PEPTIDE WITH FLUORESCEIN
  • MN12H2 IGG2A-KAPPA, light chain
  • MN12H2 IGG2A-KAPPA,heavy chain
KeywordsIMMUNE SYSTEM / MURINE IMMUNOGLOBULIN IGG2A KAPPA / BACTERICIDAL ANTIBODY / EPITOPE P1.16 OF PORA FROM NEISSERIA MENINGITIDIS / COMPLEX (IMMUNOGLOBULIN-PEPTIDE)
Function / homology
Function and homology information


immunoglobulin complex / porin activity / pore complex / immunoglobulin mediated immune response / monoatomic ion transmembrane transport / immunoglobulin complex, circulating / immunoglobulin receptor binding / B cell differentiation / complement activation, classical pathway / antigen binding ...immunoglobulin complex / porin activity / pore complex / immunoglobulin mediated immune response / monoatomic ion transmembrane transport / immunoglobulin complex, circulating / immunoglobulin receptor binding / B cell differentiation / complement activation, classical pathway / antigen binding / cell outer membrane / antibacterial humoral response / blood microparticle / immune response / extracellular space / extracellular exosome / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
Porin, Neisseria sp. type / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Porin domain, Gram-negative type / Gram-negative porin / Porin, Gram-negative type / Porin domain superfamily / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain ...Porin, Neisseria sp. type / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Porin domain, Gram-negative type / Gram-negative porin / Porin, Gram-negative type / Porin domain superfamily / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / If kappa light chain / Major outer membrane protein P.IA / Immunoglobulin kappa constant / Ig heavy chain Mem5 / Ighg protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsVan Den Elsen, J.M.H. / Herron, J.N. / Kroon, J. / Gros, P.
Citation
Journal: Proteins / Year: 1997
Title: Bactericidal antibody recognition of a PorA epitope of Neisseria meningitidis: crystal structure of a Fab fragment in complex with a fluorescein-conjugated peptide.
Authors: van den Elsen, J.M. / Herron, J.N. / Hoogerhout, P. / Poolman, J.T. / Boel, E. / Logtenberg, T. / Wilting, J. / Crommelin, D.J. / Kroon, J. / Gros, P.
#1: Journal: J.Biol.Chem. / Year: 1999
Title: Bactericidal Antibody Recognition of Meningococcal Pora by Induced Fit: Comparison of Liganded and Unliganded Fab Structures
Authors: van den Elsen, J. / Vandeputte-Rutten, L. / Kroon, J. / Gros, P.
History
DepositionJun 9, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jun 23, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 5, 2011Group: Database references / Derived calculations
Revision 1.4May 31, 2017Group: Database references / Source and taxonomy / Structure summary
Revision 1.5Aug 30, 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_conn_type / 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_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.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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: MN12H2 IGG2A-KAPPA, light chain
H: MN12H2 IGG2A-KAPPA,heavy chain
P: CONJUGATE OF PORA P1.16 PEPTIDE WITH FLUORESCEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1044
Polymers49,9923
Non-polymers1121
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-31 kcal/mol
Surface area19840 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)55.680, 69.100, 72.950
Angle α, β, γ (deg.)90.00, 112.01, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Antibody MN12H2 IGG2A-KAPPA, light chain


Mass: 24122.861 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: B-LYMPHOCYTE HYBRIDOMA / Cell line: MN12H2 MURINE-MURINE HYBRIDOMA / Strain: BALB/C / References: UniProt: P01837, UniProt: A2NHM3*PLUS
#2: Antibody MN12H2 IGG2A-KAPPA,heavy chain


Mass: 24415.350 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: B-LYMPHOCYTE HYBRIDOMA / Cell line: MN12H2 MURINE-MURINE HYBRIDOMA / Strain: BALB/C / References: UniProt: P84751, UniProt: Q569X1*PLUS
#3: Protein/peptide CONJUGATE OF PORA P1.16 PEPTIDE WITH FLUORESCEIN / P1.16 / AC-TKDTNNNLC(FLUORESCEIN)-NH2


Mass: 1453.509 Da / Num. of mol.: 1
Fragment: APEX OF EXTRACELLULAR LOOP 4 (VR2) OF PORA, RESIDUES 180 - 187
Source method: obtained synthetically
Details: SEQUENCE FROM NEISSERIA MENINGITIDIS (MENINGOCOCCUS), STRAIN: H44/76, VARIANT: P1.16;
Source: (synth.) synthetic construct (others) / References: UniProt: E6MXW0*PLUS
#4: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsCD: THIS PUTATIVE CADMIUM ION IS ASSIGNED TO A 6 SIGMA DENSITY PEAK IN A 2|FO|-|FC| MAP; IT IS ...CD: THIS PUTATIVE CADMIUM ION IS ASSIGNED TO A 6 SIGMA DENSITY PEAK IN A 2|FO|-|FC| MAP; IT IS COORDINATED BY TWO WATER MOLECULES AND AN IMIDAZOLIUM NITROGEN OF HIS-L98 OF MN12H2.
Sequence detailsREFERENCE: THE MN12H2 LIGHT CHAIN AMINO ACID SEQUENCE IS DEDUCED FROM THE GENBANK U60442 NUCLEOTIDE ...REFERENCE: THE MN12H2 LIGHT CHAIN AMINO ACID SEQUENCE IS DEDUCED FROM THE GENBANK U60442 NUCLEOTIDE SEQUENCE OF THE MN12H2 VARIABLE LIGHT DOMAIN. AMINO ACID SEQUENCES FOR THE CONSTANT DOMAINS WERE TAKEN FROM IGG2A KAPPA ANTIBODY 4-4-20 (BEDZYK ET AL. (1989) J.BIOL.CHEM., 265, P. 18615).

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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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.6
Details: THE MN12H2 FAB PEPTIDE COMPLEX WAS CRYSTALLIZED FROM 15% W/V PEG 20000, 100 MM SODIUM ACETATE, PH 4.6, 20 MM CDCL2, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: MAC Science DIP-2020 / Detector: IMAGE PLATE / Date: Mar 15, 1995 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 15404 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 16.8
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.357 / % possible all: 96.5

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HFL

2hfl
PDB Unreleased entry


Resolution: 2.6→20 Å / Data cutoff high rms absF: 100000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1397 9.09 %RANDOM
Rwork0.202 ---
obs0.202 14183 92.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 64.7 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 47.6 Å2
Baniso -1Baniso -2Baniso -3
1--6.116 Å20 Å2-18.404 Å2
2--9.264 Å20 Å2
3----3.147 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.36 Å
Luzzati d res low-20 Å
Luzzati sigma a0.48 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3506 0 1 51 3558
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.533
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.49
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.21
X-RAY DIFFRACTIONc_mcangle_it3.21.5
X-RAY DIFFRACTIONc_scbond_it3.581.5
X-RAY DIFFRACTIONc_scangle_it3.582
LS refinement shellResolution: 2.6→2.69 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.4043 163
Rwork0.3448 1133
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CAMI.PARCAMI.TOP
X-RAY DIFFRACTION3NACE.PARNACE.TOP
X-RAY DIFFRACTION4SPEP.PAR, FLU.PAR, CD.PARSPEP.TOP, FLU.TOP, CD.TOP, H20.TOP

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