[English] 日本語
Yorodumi
- PDB-1aj7: IMMUNOGLOBULIN 48G7 GERMLINE FAB ANTIBODY COMPLEXED WITH HAPTEN 5... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1aj7
TitleIMMUNOGLOBULIN 48G7 GERMLINE FAB ANTIBODY COMPLEXED WITH HAPTEN 5-(PARA-NITROPHENYL PHOSPHONATE)-PENTANOIC ACID. AFFINITY MATURATION OF AN ESTEROLYTIC ANTIBODY
Components
  • IMMUNOGLOBULIN 48G7 FAB (HEAVY CHAIN)
  • IMMUNOGLOBULIN 48G7 FAB (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN / GERMLINE ANTIBODY / FAB / CATALYTIC ANTIBODY / AFFINITY MATURATION
Function / homology
Function and homology information


Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / complement activation, classical pathway ...Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / complement activation, classical pathway / Role of phospholipids in phagocytosis / antigen binding / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / blood microparticle / adaptive immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / 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 / Immunoglobulin-like fold ...: / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
5-(PARA-NITROPHENYL PHOSPHONATE)-PENTANOIC ACID / : / Immunoglobulin heavy constant gamma 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWedemayer, G.J. / Wang, L.H. / Patten, P.A. / Schultz, P.G. / Stevens, R.C.
Citation
Journal: Science / Year: 1997
Title: Structural insights into the evolution of an antibody combining site.
Authors: Wedemayer, G.J. / Patten, P.A. / Wang, L.H. / Schultz, P.G. / Stevens, R.C.
#1: Journal: J.Mol.Biol. / Year: 1997
Title: Crystal Structures of the Free and Liganded Form of an Esterolytic Catalytic Antibody
Authors: Wedemayer, G.J. / Wang, L.H. / Patten, P.A. / Schultz, P.G. / Stevens, R.C.
#2: Journal: Science / Year: 1996
Title: The Immunological Evolution of Catalysis
Authors: Patten, P.A. / Gray, N.S. / Yang, P.L. / Marks, C.B. / Wedemayer, G.J. / Boniface, J.J. / Stevens, R.C. / Schultz, P.G.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: A Genetic Approach to the Generation of Antibodies with Enhanced Catalytic Activities
Authors: Lesley, S.A. / Patten, P.A. / Schultz, P.G.
History
DepositionMay 15, 1997Processing site: BNL
Revision 1.0Nov 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: IMMUNOGLOBULIN 48G7 FAB (LIGHT CHAIN)
H: IMMUNOGLOBULIN 48G7 FAB (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8303
Polymers46,5282
Non-polymers3021
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-22 kcal/mol
Surface area19270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.100, 60.900, 73.100
Angle α, β, γ (deg.)90.00, 104.80, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Antibody IMMUNOGLOBULIN 48G7 FAB (LIGHT CHAIN)


Mass: 23464.988 Da / Num. of mol.: 1
Fragment: VARIABLE DOMAINS OF LIGHT AND HEAVY CHAINS AND CONSTANT DOMAINS OF LIGHT AND HEAVY CHAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Description: EACH CHAIN IS A FUSION POLYPEPTIDE WHICH IS PART HUMAN AND PART MOUSE
Cell line: 48G7 / Fragment: CONSTANT DOMAINS OF LIGHT AND HEAVY CHAINS / Plasmid: PSAL143 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 4768677
#2: Antibody IMMUNOGLOBULIN 48G7 FAB (HEAVY CHAIN)


Mass: 23062.750 Da / Num. of mol.: 1
Fragment: VARIABLE DOMAINS OF LIGHT AND HEAVY CHAINS AND CONSTANT DOMAINS OF LIGHT AND HEAVY CHAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: EACH CHAIN IS A FUSION POLYPEPTIDE WHICH IS PART HUMAN AND PART MOUSE
Cell line: 48G7 / Fragment: CONSTANT DOMAINS OF LIGHT AND HEAVY CHAINS / Plasmid: PSAL143 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P01857
#3: Chemical ChemComp-NPE / 5-(PARA-NITROPHENYL PHOSPHONATE)-PENTANOIC ACID


Mass: 302.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13NO7P
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.29 %
Crystal growpH: 8
Details: 10-15 MG/ML FAB IN 100MM NACL, 10MM TRIS PH 8.0, 1MM METHIONINE, 1MM SODIUM AZIDE, 0.5 MM EDTA.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-15 mg/mlprotein1drop
2100 mM1dropNaCl
310 mMTris1drop
41 mMmethionine1drop
51 mMsodium azide1drop
60.5 mMEDTA1drop
70.1 Mammonium acetate1reservoir
80.1 Msodium cacodylate1reservoir
918 %PEG40001reservoir
101 %dioxane1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 23005 / % possible obs: 99.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 15
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 5.2 / Rsym value: 0.204 / % possible all: 98.1
Reflection
*PLUS
Num. measured all: 80267
Reflection shell
*PLUS
% possible obs: 98.1 %

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.8refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GAF

1gaf


Resolution: 2.1→20 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.258 -10 %
Rwork0.217 --
obs0.217 23005 99.5 %
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4035 0 32 0 4067
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.542
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.1→2.11 Å / Total num. of bins used: 60
RfactorNum. reflection% reflection
Rfree0.286 35 10 %
Rwork0.233 339 -

+
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