[English] 日本語
Yorodumi
- PDB-1o2f: COMPLEX OF ENZYME IIAGLC AND IIBGLC PHOSPHOCARRIER PROTEIN HPR FR... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1o2f
TitleCOMPLEX OF ENZYME IIAGLC AND IIBGLC PHOSPHOCARRIER PROTEIN HPR FROM ESCHERICHIA COLI NMR, RESTRAINED REGULARIZED MEAN STRUCTURE
Components
  • PTS system, glucose-specific IIA component
  • PTS system, glucose-specific IIBC component
KeywordsTRANSFERASE / PHOSPHOTRANSFERASE / KINASE / SUGAR TRANSPORT / COMPLEX (TRANSFERASE-PHOSPHOCARRIER)
Function / homology
Function and homology information


protein-phosphocysteine-glucose phosphotransferase system transporter activity / protein-Npi-phosphohistidine-D-glucose phosphotransferase / negative regulation of carbohydrate metabolic process / glucose transmembrane transporter activity / protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / negative regulation of maltose transport / enzyme IIA-maltose transporter complex / glucose import across plasma membrane / negative regulation of transmembrane transport / glucose transmembrane transport ...protein-phosphocysteine-glucose phosphotransferase system transporter activity / protein-Npi-phosphohistidine-D-glucose phosphotransferase / negative regulation of carbohydrate metabolic process / glucose transmembrane transporter activity / protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / negative regulation of maltose transport / enzyme IIA-maltose transporter complex / glucose import across plasma membrane / negative regulation of transmembrane transport / glucose transmembrane transport / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / kinase activity / phosphorylation / regulation of DNA-templated transcription / membrane / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Glucose permease domain IIB / Phosphotransferase system, maltose/glucose-specific subfamily IIC component / PTS system glucose-specific IIBC component / Phosphotransferase system, IIB component, type 1 / Phosphotransferase system, EIIC component, type 1 / Phosphotransferase system EIIB, cysteine phosphorylation site / Glucose permease domain IIB / phosphotransferase system, EIIB / PTS EIIB domains cysteine phosphorylation site signature. / PTS_EIIB type-1 domain profile. ...Glucose permease domain IIB / Phosphotransferase system, maltose/glucose-specific subfamily IIC component / PTS system glucose-specific IIBC component / Phosphotransferase system, IIB component, type 1 / Phosphotransferase system, EIIC component, type 1 / Phosphotransferase system EIIB, cysteine phosphorylation site / Glucose permease domain IIB / phosphotransferase system, EIIB / PTS EIIB domains cysteine phosphorylation site signature. / PTS_EIIB type-1 domain profile. / PTS_EIIC type-1 domain profile. / Phosphotransferase system, EIIC / Phosphotransferase system, EIIC / PTS EIIA domains phosphorylation site signature 1. / Phosphotransferase system, sugar-specific permease EIIA type 1 / phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1 / PTS_EIIA type-1 domain profile. / Glucose Permease (Domain IIA) / Glucose Permease (Domain IIA) / Duplicated hybrid motif / Gyrase A; domain 2 / Distorted Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHITE ION / PTS system glucose-specific EIIA component / PTS system glucose-specific EIICB component
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / CONJOINED RIGID BODY, TORSION ANGLE DYNAMICS
AuthorsClore, G.M. / Cai, M. / Williams, D.C.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Solution Structure of the Phosphoryl Transfer Complex between the Signal-transducing Protein IIAGlucose and the Cytoplasmic Domain of the Glucose Transporter IICBGlucose of the Escherichia ...Title: Solution Structure of the Phosphoryl Transfer Complex between the Signal-transducing Protein IIAGlucose and the Cytoplasmic Domain of the Glucose Transporter IICBGlucose of the Escherichia coli Glucose Phosphotransferase System.
Authors: Cai, M. / Williams Jr., D.C. / Wang, G. / Lee, B.R. / Peterkofsky, A. / Clore, G.M.
History
DepositionMar 11, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jun 30, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description
Category: atom_site / pdbx_nmr_refine ...atom_site / pdbx_nmr_refine / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_planes / pdbx_validate_torsion / struct_asym
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.pdbx_PDB_model_num / _atom_site.type_symbol / _pdbx_nmr_refine.details / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_validate_close_contact.PDB_model_num / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_close_contact.dist / _pdbx_validate_planes.rmsd / _pdbx_validate_torsion.PDB_model_num / _pdbx_validate_torsion.auth_asym_id / _pdbx_validate_torsion.auth_comp_id / _pdbx_validate_torsion.auth_seq_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PTS system, glucose-specific IIA component
B: PTS system, glucose-specific IIBC component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4773
Polymers27,3982
Non-polymers791
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1140 Å2
ΔGint-6 kcal/mol
Surface area10630 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)3 / 60REGULARIZED MEAN STRUCTURES
Representative

-
Components

#1: Protein PTS system, glucose-specific IIA component / IIAGLC / EIIA-GLC / Glucose-permease IIA component / Phosphotransferase enzyme II / A component / EIII-GLC


Mass: 18141.834 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: P69783, protein-Npi-phosphohistidine-sugar phosphotransferase
#2: Protein PTS system, glucose-specific IIBC component / IIBGLC / EIIBC-Glc / Glucose-permease IIBC component / Phosphotransferase enzyme II / BC component / EII-Glc


Mass: 9256.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: P69786, protein-Npi-phosphohistidine-sugar phosphotransferase
#3: Chemical ChemComp-PO3 / PHOSPHITE ION / Phosphite ester


Mass: 78.972 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO3

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111) TRIPLE RESONANCE FOR ASSIGNMENT OF PROTEIN
121(2) QUANTITATIVE J CORRELATION FOR COUPLING CONSTANTS
131(3) 3D
1414D HETERONUCLEAR SEPARATED
151FILTERED NOE EXPTS
161(4) IPAP EXPERIMENTS FOR DIPOLAR COUPLINGS. DIPOLAR COUPLINGS WERE MEASURED IN PHAGE PF1

-
Sample preparation

Sample conditionsIonic strength: 10 mM SODIUM PHOSPHATE / pH: 7.0 / Temperature: 308.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE DMXBrukerAVANCE DMX5001
Bruker AVANCE DMXBrukerAVANCE DMX6002
Bruker AVANCE DRXBrukerAVANCE DRX7503
Bruker AVANCE DRXBrukerAVANCE DRX8004
Bruker AVANCE DRXBrukerAVANCE DRX8005

-
Processing

NMR softwareName: X-PLOR NIH / Version: (HTTP://NMR.CIT.NIH.GOV/XPLOR_NIH)
Developer: SCHWIETERS, KUSZEWSKI, TJANDRA, CLORE J.MAGN.RESON. 160, 66-73 (2003)
Classification: refinement
RefinementMethod: CONJOINED RIGID BODY, TORSION ANGLE DYNAMICS / Software ordinal: 1
Details: THE STRUCTURES WERE CALCULATED BY CONJOINED RIGID BODY/TORSION ANGLE DYNAMICS (SCHWIETERS & CLORE (2001) J.MAGN.RESON 152, 288-302). THE TARGET FUNCTIONS COMPRISES TERMS FOR THE NOE-DERIVED ...Details: THE STRUCTURES WERE CALCULATED BY CONJOINED RIGID BODY/TORSION ANGLE DYNAMICS (SCHWIETERS & CLORE (2001) J.MAGN.RESON 152, 288-302). THE TARGET FUNCTIONS COMPRISES TERMS FOR THE NOE-DERIVED TERMS FOR THE NOE RESTRAINTS (INTRA AND INTERMOLECULAR), THE INTERFACIAL SIDECHAIN TORSION ANGLE RESTRAINTS FOR IIAGLC, THE BACKBONE AND SIDE CHAIN TORSION ANGLE RESTRAINTS FOR IIBGLC, THE DIPOLAR COUPLING RESTRAINTS FOR IIBGL (CLORE ET AL. J.MAGN.RESON. 131, 159-162 (1998); J.MAGN.RESON. 133, 216-221(1998)), THE RADIUS OF GYRATION (KUSZEWSKI ET AL. (1999), A QUARTIC VAN DER WAALS REPULSION TERM (NILGES ET AL. (1988) FEBS LETT. 229, 129- 136), AND A TORSION ANGLE DATABASE POTENTIAL OF MEAN FORCE (CLORE & KUSZEWSKI (2002) J.AM.CHEM.SOC 121, 2337-2338). THE STARTING COORDINATES FOR IIAGLC ARE FROM THE 2.1 ANGSTROM RESOLUTION X-RAY STRUCTURE (WITH PROTONS ADDED) OF E. COLI IIAGLC (MOLECULE 2 OF 2F3G; FEESE ET AL. BIOCHEMISTRY 36, 16087-16096 (1997)). THE BACKBONE COORDINATES AND NON- INTERFACIAL SIDECHAINS OF IIAGLC ARE TREATED AS A RIGID BODY. IN THIS ENTRY THE LAST COLUMN REPRESENTS THE AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL SIMULATED ANNEALING STRUCTURES AND THE MEAN COORDINATE POSITIONS. IT IS IMPORTANT TO NOTE THAT THE VALUES GIVEN FOR THE BACKBONE ATOMS AND NON-INTERFACIAL SIDECHAINS OF IIAGLC PROVIDE ONLY A MEASURE OF THE PRECISION WITH WHICH THE RELATIVE ORIENTATION OF IIAGLC IN THE COMPLEX HAS BEEN DETERMINED AND DOES NOT TAKE INTO ACCOUNT THE THE ERRORS IN THE X-RAY COORDINATES OF IIAGLC RESIDUE NUMBERING: IIAGLC: 19-168 (RESIDUES 1-18 ARE DISORDERED IN SOLUTION AND NOT VISIBLE IN THE ELECTRON DENSITY MAP OF THE CRYSTAL STRUCTURE OF THE FREE PROTEIN). IIBGLC: 314-390 (CORRESPONDING TO RESIDUES 400-476 OF INTACT IIBCGLC. RESIDUES 301-314 ARE DISORDERED IN SOLUTION. PRO317 HAS BEEN MUTATED TO ALA TO REMOVE HETEROGENEITY ARISING FROM CIS-TRANS PROLINE ISOMERIZATION. PHOSPHATE: RESIDUE 200 EXPERIMENTAL RESTRAINTS: INTRAMOLECULAR INTERPROTON DISTANCE RESTRAINTS: IIBGLC: 987 (189 INTRARESIDUE, 273 SEQUENTIAL, (218 MEDIUM RANGE (1 < |I-J|<=5, 307 LONG RANGE (|I-J>5) IIAGLC INTERFACIAL SIDE CHAINS: 30 INTERMOLECULAR INTERPROTON DISTANCE RESTRAINTS: 113 BACKBONE H-BOND RESTRAINTS FOR IIBGLC (2 PER H-BOND): 72 TORSION ANGLE RESTRAINTS: IIBGLC: 221 IIAGLC INTERFACIAL SIDE CHAINS: 34 RESIDUAL DIPOLAR COUPLINGS FOR IIBGLC: 174 (58 N-H, 58 N-C', 58 HN-C') 13CALPHA/BETA SHIFTS FOR IIBGLC: 138 THREE SETS OF COORDINATES ARE GIVEN: MODEL 3: RESTRAINED REGULARIZED MEAN COORDINATES OF THE UNPHOSPHORYLATED IIAGLC-IIBGLC COMPLEX OVERALL BACKBONE COORDINATE PRECISION (IIAGLC+IIBGLC): 0.31A HEAVY ATOM INTERFACE SIDECHAIN COORDINATE PRECISION (IIAGLC+IIBGLC): 0.67A BACKBONE COORDINATE PRECISION FOR IIBGLC: 0.21 A ALL HEAVY ATOM COORDINATE PRECISION FOR IIBGLC; 0.71 A MODEL 2: RESTRAINED REGULARIZED MEAN COORDINATES FOR THE MODEL OF THE DISSOCIATIVE PHOSPHORYL TRANSITION STATE IIAGLC-IIBGLC. EXPERIMENTAL RESTRAINTS ARE IDENTICAL TO THOSE USED FOR MODEL 3, BUT COVALENT GEOMETRY RESTRAINTS ARE INCLUDED RELATING TO THE PENTACOORDINATE PHOSPHORYL GROUP IN A TRIGONAL BIPYRAMIDAL GEOMETRY. THE STRUCTURE IS DERIVED FROM MODEL 3 BY RESTRAINED CONJOINED TORSION ANGLE/RIGID BODY MINIMIZATION. NO RESTRAINTS WERE EMPLOYED FOR THE NE2(HIS90/IIAGLC)-P AND SG(CYS35/IIBGLC)-P DISTANCES. THERE IS NO CHANGE IN BACKBONE RELATIVE TO MODEL 3 BUT THE NE2(HIS90/IIAGLC- SG(CYS35/IIBGLC) DISTANCE IS REDUCED FROM 5.75 A IN MODEL 3 TO 5.3 A IN MODEL 2. MODEL 1: RESTRAINED REGULARIZED MEAN COORDINATES FOR THE MODEL OF THE ASSOCIATIVE PHOSPHORYL TRANSITION STATE HPR-IIAGLC COMPLEX. CALCULATED LIKE MODEL 2 BUT WITH THE NE2(HIS90/IIAGLC)-P AND SG(CYS35/IIBGLC)-P DISTANCES RESTRAINED TO 2 A. THE STRUCTURE IS DERIVED FROM MODEL 3 BY RESTRAINED CONJOINED TORSION ANGLE/RIGID BODY MINIMIZATION. THE RMS DIFFERENCE BETWEEN THE MEAN STRUCTURES OF THE UNPHOSPHORYLATED COMPLEX (MODEL 3) AND THE TRANSITION STATE COMPLEX (MODEL 1) IS ONLY 0.1 A FOR BACKBONE COORDINATES IMMEDIATELY ADJACENT TO THE ACTIVE SITE HIS AND CYS (RESIDUES 89-91 OF IIAGLC AND 334-336 of IIBGLC). THE REMAINING BACKBONE COORDINATES DO NOT SHIFT.
NMR ensembleConformer selection criteria: REGULARIZED MEAN STRUCTURES / Conformers calculated total number: 60 / Conformers submitted total number: 3
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg10
X-RAY DIFFRACTIONx_dihedral_angle_d10
X-RAY DIFFRACTIONx_improper_angle_d

+
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