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- PDB-1mpa: BACTERICIDAL ANTIBODY AGAINST NEISSERIA MENINGITIDIS -

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Basic information

Entry
Database: PDB / ID: 1mpa
TitleBACTERICIDAL ANTIBODY AGAINST NEISSERIA MENINGITIDIS
Components
  • (MN12H2 IGG2A-KAPPA) x 2
  • PORA P1.16 PEPTIDE FLUORESCEIN CONJUGATE
KeywordsCOMPLEX (IMMUNOGLOBULIN/PEPTIDE) / MURINE IMMUNOGLOBULIN IGG2A KAPPA / BACTERICIDAL ANTIBODY / EPITOPE P1.16 OF PORA FROM NEISSERIA MENINGITIDIS / COMPLEX (IMMUNOGLOBULIN-PEPTIDE) / COMPLEX (IMMUNOGLOBULIN-PEPTIDE) complex
Function / homology
Function and homology information


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 ...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 / Ighg protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsVan Den Elsen, J.M.H. / Herron, J.N. / Kroon, J. / Gros, P.
CitationJournal: 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.
History
DepositionFeb 26, 1997Processing site: BNL
Revision 1.0Sep 4, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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_ref_seq_dif.details / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: MN12H2 IGG2A-KAPPA
H: MN12H2 IGG2A-KAPPA
P: PORA P1.16 PEPTIDE FLUORESCEIN CONJUGATE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1044
Polymers49,9923
Non-polymers1121
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-30 kcal/mol
Surface area19480 Å2
MethodPISA
2
P: PORA P1.16 PEPTIDE FLUORESCEIN CONJUGATE

L: MN12H2 IGG2A-KAPPA
H: MN12H2 IGG2A-KAPPA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1044
Polymers49,9923
Non-polymers1121
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation1_554x,y,z-11
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-33 kcal/mol
Surface area20210 Å2
MethodPISA
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
Space group name H-MP1211

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Components

#1: Antibody MN12H2 IGG2A-KAPPA


Mass: 24122.861 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/C / Cell: B-LYMPHOCYTE HYBRIDOMA
Cell line (production host): MN12H2 MURINE-MURINE HYBRIDOMA CELL LINE
Production host: Mus musculus (house mouse) / References: PIR: PC4203, UniProt: A2NHM3*PLUS
#2: Antibody MN12H2 IGG2A-KAPPA


Mass: 24415.350 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/C / Cell: B-LYMPHOCYTE HYBRIDOMA
Cell line (production host): MN12H2 MURINE-MURINE HYBRIDOMA CELL LINE
Production host: Mus musculus (house mouse) / References: PIR: S38950, UniProt: Q569X1*PLUS
#3: Protein/peptide PORA P1.16 PEPTIDE FLUORESCEIN CONJUGATE / 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: isolated from a genetically manipulated source
#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 / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growpH: 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 CDCL.
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 1, 1995 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / 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 % / Biso Wilson estimate: 37.1 Å2 / 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
Reflection
*PLUS
Num. measured all: 94382
Reflection shell
*PLUS
% possible obs: 96.5 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.63refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HFL

2hfl
PDB Unreleased entry


Resolution: 2.6→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.309 1397 9.09 %RANDOM
Rwork0.194 ---
obs0.194 14183 92.3 %-
Displacement parametersBiso mean: 27.9 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å / Luzzati d res low obs: 8 Å / Luzzati sigma a obs: 0.46 Å
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3532 0 1 17 3550
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.812
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.44
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.38
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.21
X-RAY DIFFRACTIONx_mcangle_it3.21.5
X-RAY DIFFRACTIONx_scbond_it3.581.5
X-RAY DIFFRACTIONx_scangle_it3.582
LS refinement shellResolution: 2.6→2.71 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.41 163 8.53 %
Rwork0.34 1384 -
obs--80.95 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
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
Software
*PLUS
Name: X-PLOR / Version: 3.63 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.44
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.38
LS refinement shell
*PLUS
Rfactor obs: 0.34

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