[English] 日本語
Yorodumi
- PDB-1f3z: IIAGLC-ZN COMPLEX -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1f3z
TitleIIAGLC-ZN COMPLEX
ComponentsGLUCOSE-SPECIFIC PHOSPHOCARRIER
KeywordsPHOSPHOTRANSFERASE / SIGNAL TRANSDUCTION / SUGAR TRANSPORT
Function / homology
Function and homology information


negative regulation of carbohydrate metabolic process / regulation of carbohydrate utilization / negative regulation of maltose transport / enzyme IIA-maltose transporter complex / negative regulation of transmembrane transport / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / kinase activity / metal ion binding / membrane / cytosol
Similarity search - Function
: / 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 / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
PTS system glucose-specific EIIA component
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsFeese, M. / Comolli, L. / Meadow, N. / Roseman, S. / Remington, S.J.
CitationJournal: Biochemistry / Year: 1997
Title: Structural studies of the Escherichia coli signal transducing protein IIAGlc: implications for target recognition.
Authors: Feese, M.D. / Comolli, L. / Meadow, N.D. / Roseman, S. / Remington, S.J.
History
DepositionOct 9, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GLUCOSE-SPECIFIC PHOSPHOCARRIER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4032
Polymers17,3381
Non-polymers651
Water41423
1
A: GLUCOSE-SPECIFIC PHOSPHOCARRIER
hetero molecules

A: GLUCOSE-SPECIFIC PHOSPHOCARRIER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8074
Polymers34,6762
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_775-y+2,-x+2,-z+1/21
Unit cell
Length a, b, c (Å)47.700, 47.700, 144.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein GLUCOSE-SPECIFIC PHOSPHOCARRIER / EIIA-GLC


Mass: 17337.842 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: IIAGLC FAST-MISSING SEVEN N-TERMINAL AMINO ACIDS / Source: (natural) Escherichia coli (E. coli)
References: UniProt: P69783, protein-Npi-phosphohistidine-sugar phosphotransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.28 Å3/Da / Density % sol: 48.12 %
Crystal growpH: 8.5
Details: 0.1-0.3 M SODIUM ACETATE, 1MM ZINC ACETATE, 0.1 M TRIS BUFFER PH 8.5
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
122-26 %PEG400011
20.1-0.3 Msodium acetate11
31 mMzinc acetate11
40.1 MTris-HCl11
56 mg/mlprotain12

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 1, 1994
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.98→20 Å / Num. obs: 7578 / % possible obs: 61 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 41.5 Å2 / Rmerge(I) obs: 0.044
Reflection
*PLUS
Num. measured all: 22910

-
Processing

Software
NameVersionClassification
UNPUBLISHEDmodel building
TNT5Erefinement
DENZOdata reduction
SCALEPACKdata scaling
UNPUBLISHEDphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F3G

1f3g


Resolution: 1.98→20 Å / Isotropic thermal model: TNT BCORREL V2.1 / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
Rwork0.193 --
all-7578 -
obs-7578 61 %
Solvent computationSolvent model: BABINET SCALING / Bsol: 300 Å2 / ksol: 0.8 e/Å3
Refinement stepCycle: LAST / Resolution: 1.98→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1107 0 1 23 1131
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01111221.5
X-RAY DIFFRACTIONt_angle_deg1.9815183
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.009282
X-RAY DIFFRACTIONt_gen_planes0.0151616
X-RAY DIFFRACTIONt_it5.711221.5
X-RAY DIFFRACTIONt_nbd0.0222510
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 5.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_planar_d0.0092
X-RAY DIFFRACTIONt_plane_restr0.0156

+
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