[English] 日本語
Yorodumi
- PDB-2jel: JEL42 FAB/HPR COMPLEX -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jel
TitleJEL42 FAB/HPR COMPLEX
Components
  • (JEL42 FAB FRAGMENT) x 2
  • HISTIDINE-CONTAINING PROTEIN
KeywordsCOMPLEX (ANTIBODY/ANTIGEN) / ANTIBODY-PROTEIN COMPLEX / HISTIDINE-CONTAINING PROTEIN / MOLECULAR RECOGNITION / COMPLEX (ANTIBODY-ANTIGEN) / COMPLEX (ANTIBODY-ANTIGEN) complex
Function / homology
Function and homology information


phosphotransferase activity, nitrogenous group as acceptor / antisigma factor binding / regulation of carbon utilization / positive regulation of glycogen catabolic process / phosphoenolpyruvate-dependent sugar phosphotransferase system / enzyme inhibitor activity / enzyme regulator activity / enzyme activator activity / cytosol
Similarity search - Function
Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / HPr-like / Phosphocarrier protein HPr-like / HPr-like superfamily / : / PTS HPr component phosphorylation site / PTS HPR domain profile. / Histidine-containing Protein; Chain: A; ...Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / HPr-like / Phosphocarrier protein HPr-like / HPr-like superfamily / : / PTS HPr component phosphorylation site / PTS HPR domain profile. / Histidine-containing Protein; Chain: A; / PTS HPR domain serine phosphorylation site signature. / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Phosphocarrier protein HPr
Similarity search - Component
Biological speciesMus musculus (house mouse)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPrasad, L. / Waygood, E.B. / Lee, J.S. / Delbaere, L.T.J.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: The 2.5 A resolution structure of the jel42 Fab fragment/HPr complex
Authors: Prasad, L. / Waygood, E.B. / Lee, J.S. / Delbaere, L.T.J.
#1: Journal: J.Biol.Chem. / Year: 1993
Title: Evaluation of Mutagenesis for Epitope Mapping. Structure of an Antibody-Protein Antigen Complex
Authors: Prasad, L. / Sharma, S. / Vandonselaar, M. / Quail, J.W. / Lee, J.S. / Waygood, E.B. / Wilson, K.S. / Dauter, Z. / Delbaere, L.T.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991
Title: Epitope Mapping by Mutagenesis Distinguishes between the Two Tertiary Structures of the Histidine-Containing Protein Hpr
Authors: Sharma, S. / Georges, F. / Delbaere, L.T. / Lee, J.S. / Klevit, R.E. / Waygood, E.B.
#3: Journal: J.Biol.Chem. / Year: 1989
Title: Crystallization of the Complex of a Monoclonal Fab Fragment with the Histidine-Containing Protein of the Phosphoenolpyruvate: Sugar Phosphotransferase System of Escherichia Coli
Authors: Delbaere, L.T. / Vandonselaar, M. / Quail, J.W. / Waygood, E.B. / Lee, J.S.
#4: Journal: J.Biol.Chem. / Year: 1988
Title: Structure Determination of a Monoclonal Fab Fragment Specific for Histidine-Containing Protein of the Phosphoenolpyruvate: Sugar Phosphotransferase System of Escherichia Coli
Authors: Prasad, L. / Vandonselaar, M. / Lee, J.S. / Delbaere, L.T.
History
DepositionFeb 24, 1998Processing site: BNL
SupersessionMay 27, 1998ID: 1JEL
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Other / Refinement description / Category: diffrn_detector / pdbx_database_status / software
Item: _diffrn_detector.detector / _pdbx_database_status.process_site / _software.name
Revision 1.4Apr 3, 2024Group: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: JEL42 FAB FRAGMENT
H: JEL42 FAB FRAGMENT
P: HISTIDINE-CONTAINING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2765
Polymers56,0843
Non-polymers1922
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-53 kcal/mol
Surface area22880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.850, 67.380, 77.090
Angle α, β, γ (deg.)90.00, 97.34, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Antibody JEL42 FAB FRAGMENT


Mass: 23860.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C
#2: Antibody JEL42 FAB FRAGMENT


Mass: 23094.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C
#3: Protein HISTIDINE-CONTAINING PROTEIN / HPR


Mass: 9129.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0AA04
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRESIDUES OF THE FAB FRAGMENT ARE NUMBERED ACCORDING TO KABAT.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 57 %
Crystal growpH: 5.8 / Details: pH 5.8
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Details: the molar ratio of Fab fragment to HPr was approximately 1:2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlFab fragment1drop
24 mg/mlHPr1drop
325 %satammonium sulfate1drop
425 mMphosphate1drop

-
Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Apr 1, 1992 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→35 Å / Num. obs: 22067 / % possible obs: 96.6 % / Observed criterion σ(I): 5 / Redundancy: 2.7 % / Rsym value: 0.046 / Net I/σ(I): 11
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.19 / % possible all: 93
Reflection
*PLUS
Num. measured all: 47817 / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
% possible obs: 93 % / Num. unique obs: 1043 / Num. measured obs: 2784 / Rmerge(I) obs: 0.19

-
Processing

Software
NameVersionClassification
MADNESdata collection
Agrovata(CCP4)data reduction
X-PLOR3.1model building
X-PLOR3.1refinement
MADNESdata reduction
Agrovatadata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: GLOOP2 FAB

Resolution: 2.5→6 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: INDIVIDUAL ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1014 5 %RANDOM
Rwork0.21 ---
obs0.21 20427 96 %-
Displacement parametersBiso mean: 36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.25 Å
Luzzati d res low-6 Å
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3937 0 10 67 4014
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.2
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.322.85
X-RAY DIFFRACTIONx_mcangle_it4.644.5
X-RAY DIFFRACTIONx_scbond_it5.244.91
X-RAY DIFFRACTIONx_scangle_it6.847
LS refinement shellResolution: 2.5→2.56 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.39 114 4.9 %
Rwork0.34 1043 -
obs--93 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / 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
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.2
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