[English] 日本語
Yorodumi
- PDB-7x7h: Crystal structure of Fructose regulator/Histidine phosphocarrier ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7x7h
TitleCrystal structure of Fructose regulator/Histidine phosphocarrier protein complex from Vibrio cholerae
Components
  • Catabolite repressor/activator
  • HPr family phosphocarrier protein
KeywordsGENE REGULATION/TRANSFERASE / PTS / Vibrio / fructose / transcriptional regulator / GalR/LacI / HPr / GENE REGULATION / GENE REGULATION-TRANSFERASE complex
Function / homology
Function and homology information


Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases / phosphoenolpyruvate-dependent sugar phosphotransferase system / response to fructose / transferase activity / regulation of DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
D-fructose-responsive transcription factor / Periplasmic binding protein/LacI sugar binding domain / Periplasmic binding proteins and sugar binding domain of LacI family / Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / PTS HPR domain serine phosphorylation site signature. / Phosphocarrier protein HPr-like / HPr-like superfamily / PTS HPr component phosphorylation site ...D-fructose-responsive transcription factor / Periplasmic binding protein/LacI sugar binding domain / Periplasmic binding proteins and sugar binding domain of LacI family / Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / Phosphotransferase system, HPr serine phosphorylation site / PTS HPR domain serine phosphorylation site signature. / Phosphocarrier protein HPr-like / HPr-like superfamily / PTS HPr component phosphorylation site / PTS HPR domain profile. / LacI-type HTH domain signature. / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / Lambda repressor-like, DNA-binding domain superfamily / Periplasmic binding protein-like I
Similarity search - Domain/homology
HPr family phosphocarrier protein / Catabolite repressor/activator
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKim, M.-K. / Zhang, J. / Yoon, C.-K. / Seok, Y.-J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2020R1F1A1057780 Korea, Republic Of
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: HPr prevents FruR-mediated facilitation of RNA polymerase binding to the fru promoter in Vibrio cholerae.
Authors: Yoon, C.K. / Lee, S.H. / Zhang, J. / Lee, H.Y. / Kim, M.K. / Seok, Y.J.
History
DepositionMar 9, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Catabolite repressor/activator
B: HPr family phosphocarrier protein
C: Catabolite repressor/activator
D: HPr family phosphocarrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0496
Polymers91,9684
Non-polymers802
Water8,035446
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.940, 62.355, 312.669
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Catabolite repressor/activator


Mass: 36033.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: cra, D6U24_17570, EYB64_06550, FLM02_11955, FXE67_10910, HPY07_16365
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F0B292
#2: Protein HPr family phosphocarrier protein / PTS sugar transporter / Phosphocarrier protein HPr


Mass: 9950.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: ptsH, BC353_05360, D6U24_08050, ERS013138_01023, ERS013165_01775, ERS013166_02939, ERS013186_02269, ERS013193_00498, ERS013198_00582, ERS013199_02080, ERS013200_03874, ERS013201_03670, ...Gene: ptsH, BC353_05360, D6U24_08050, ERS013138_01023, ERS013165_01775, ERS013166_02939, ERS013186_02269, ERS013193_00498, ERS013198_00582, ERS013199_02080, ERS013200_03874, ERS013201_03670, ERS013202_02606, ERS013206_00437, ERS013207_01739, EYB64_14625, F0315_00300, F0H40_04200, F0M16_13080, FLM02_01405, FLM12_04230, FXE67_16935, HPY07_09360
Production host: Escherichia coli (E. coli)
References: UniProt: A0A085PY40, Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 446 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDescription: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
Crystal growTemperature: 295 K / Method: microbatch / Details: calcium acetate, PEG 3350, spermidine

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 46109 / % possible obs: 100 % / Redundancy: 7.6 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.996 / Rpim(I) all: 0.036 / Rrim(I) all: 0.138 / Χ2: 0.05 / Net I/av σ(I): 31.294 / Net I/σ(I): 6.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2-2.037.60.8014.73342210.8770.9670.2240.8551.381100
2.03-2.077.60.65843111.413100
2.07-2.117.60.56143781.494100
2.11-2.157.60.51142981.519100
2.15-2.27.60.44242671.517100
2.2-2.257.60.41643741.567100
2.25-2.317.60.38642841.588100
2.31-2.377.60.33643231.608100
2.37-2.447.60.30343641.634100
2.44-2.527.60.25842171.686100
2.52-2.617.60.23844121.673100
2.61-2.717.60.21342781.746100
2.71-2.847.70.18143661.816100
2.84-2.997.60.14542241.896100
2.99-3.177.70.11543202.02100
3.17-3.427.60.08743592.141100
3.42-3.767.60.07643072.324100
3.76-4.317.60.06342942.487100
4.31-5.437.60.05943252.403100
5.43-507.30.06143272.74499.6

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RZR

1rzr


Resolution: 2→31.13 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.91 / Stereochemistry target values: ML
Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.2266 2000 4.34 %
Rwork0.1788 --
obs0.1809 46109 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→31.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5440 0 2 446 5888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d0.939
X-RAY DIFFRACTIONf_dihedral_angle_d5.589756
X-RAY DIFFRACTIONf_chiral_restr0.049876
X-RAY DIFFRACTIONf_plane_restr0.006978
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.28811350.23462978X-RAY DIFFRACTION99
2.05-2.110.25041410.19933117X-RAY DIFFRACTION100
2.11-2.170.26611410.19423083X-RAY DIFFRACTION100
2.17-2.240.2481400.18593121X-RAY DIFFRACTION100
2.24-2.320.24561400.19053070X-RAY DIFFRACTION100
2.32-2.410.26621430.18953149X-RAY DIFFRACTION100
2.41-2.520.23481390.18443085X-RAY DIFFRACTION100
2.52-2.660.24911430.18883149X-RAY DIFFRACTION100
2.66-2.820.23161440.18833176X-RAY DIFFRACTION100
2.82-3.040.23911420.19523120X-RAY DIFFRACTION100
3.04-3.340.24721430.17583172X-RAY DIFFRACTION100
3.34-3.830.21041470.15913215X-RAY DIFFRACTION100
3.83-4.820.15281470.14143249X-RAY DIFFRACTION100
4.82-31.130.23461550.19143425X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -8.4218 Å / Origin y: -14.2757 Å / Origin z: 41.0611 Å
111213212223313233
T0.0837 Å20.0052 Å2-0.0074 Å2-0.1443 Å20.0011 Å2--0.1652 Å2
L0.3284 °20.026 °2-0.1031 °2-0.6115 °20.0339 °2--0.8246 °2
S-0.0248 Å °0.0365 Å °0.0338 Å °-0.0523 Å °0.0457 Å °0.0144 Å °-0.0328 Å °-0.0103 Å °-0.0213 Å °
Refinement TLS groupSelection details: all

+
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://pdbjlvh1.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