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- PDB-1mnu: UNLIGANDED BACTERICIDAL ANTIBODY AGAINST NEISSERIA MENINGITIDIS -

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Basic information

Entry
Database: PDB / ID: 1mnu
TitleUNLIGANDED BACTERICIDAL ANTIBODY AGAINST NEISSERIA MENINGITIDIS
Components
  • PROTEIN (IGG2A-KAPPA ANTIBODY MN12H2 (HEAVY CHAIN))
  • PROTEIN (IGG2A-KAPPA ANTIBODY MN12H2 (LIGHT CHAIN))
KeywordsIMMUNE SYSTEM / MURINE IMMUNOGLOBULIN IGG2A KAPPA / BACTERICIDAL ANTIBODY / EPITOPE P1.16 OF PORA FROM NEISSERIA MENINGITIDIS / UNLIGANDED
Function / homology
Function and homology information


immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / metal ion binding
Similarity search - Function
: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type ...: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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 / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / If kappa light chain / Ig gamma-2A chain C region, A allele
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsVan Den Elsen, J. / Vandeputte-Rutten, L. / Kroon, J. / Gros, P.
CitationJournal: 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
DepositionApr 30, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0May 6, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.4Feb 6, 2019Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Source and taxonomy
Category: chem_comp / entity_src_nat ...chem_comp / entity_src_nat / exptl_crystal_grow / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num ..._entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _exptl_crystal_grow.temp / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_end
Revision 1.5Dec 27, 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.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_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 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: PROTEIN (IGG2A-KAPPA ANTIBODY MN12H2 (LIGHT CHAIN))
H: PROTEIN (IGG2A-KAPPA ANTIBODY MN12H2 (HEAVY CHAIN))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8755
Polymers48,5382
Non-polymers3373
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-45 kcal/mol
Surface area19860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.617, 85.862, 87.133
Angle α, β, γ (deg.)90.00, 122.69, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody PROTEIN (IGG2A-KAPPA ANTIBODY MN12H2 (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: A2NHM3*PLUS
#2: Antibody PROTEIN (IGG2A-KAPPA ANTIBODY MN12H2 (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: P01863*PLUS
#3: Chemical ChemComp-CD / CADMIUM ION


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


Mass: 18.015 Da / Num. of mol.: 173 / 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: 3.6 Å3/Da / Density % sol: 66 %
Crystal growTemperature: 277 K / pH: 6.3
Details: THE UNLIGANDED MN12H2 FAB WAS CRYSTALLIZED FROM 20% V/V MPD, 50 MM MES BUFFER, PH 6.3, 20 MM CDCL2.
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 %(v/v)MPD1reservoir
220 mM1reservoirCdCl2
350 mMMES1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: MAC Science DIP-2020 / Detector: IMAGE PLATE / Date: Mar 1, 1998 / 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: 2.5→20 Å / Num. obs: 15404 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 13.2
Reflection shellResolution: 2.29→2.5 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.8 / Rsym value: 0.32 / % possible all: 99
Reflection
*PLUS
Num. obs: 24598 / % possible obs: 100 % / Num. measured all: 176951

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MPA

1mpa


Resolution: 2.5→20 Å / Data cutoff high rms absF: 100000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.27 2417 9.8 %RANDOM
Rwork0.231 ---
obs-24596 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 27 Å2 / ksol: 0.316 e/Å3
Displacement parametersBiso mean: 27.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å2-3.07 Å2
2---4.04 Å20 Å2
3---4.639 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.38 Å
Luzzati sigma a0.34 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3387 0 6 170 3563
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_deg1.624
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.34
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.787
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: 2.5→2.59 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.364 253
Rwork0.316 2131
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CD.PARCD.TOP
X-RAY DIFFRACTION3H2O.PARH2O.PAR
Software
*PLUS
Name: CNS / Version: 3.63 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.231 / Rfactor Rfree: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.34
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.787
X-RAY DIFFRACTIONc_mcbond_it3.2
X-RAY DIFFRACTIONc_mcangle_it3.2

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