[English] 日本語
Yorodumi
- PDB-1mpa: BACTERICIDAL ANTIBODY AGAINST NEISSERIA MENINGITIDIS -

+
Open data


ID or keywords:

Loading...

-
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/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type ...: / : / 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
: / : / : / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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 %

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more