[English] 日本語
Yorodumi
- PDB-5jeq: Fragment of nitrate/nitrite sensor histidine kinase NarQ (R50K) i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jeq
TitleFragment of nitrate/nitrite sensor histidine kinase NarQ (R50K) in symmetric apo state
ComponentsNitrate/nitrite sensor protein NarQ
KeywordsTRANSFERASE / membrane protein / sensor / histidine kinase / nitrate
Function / homology
Function and homology information


cellular response to nitrate / cellular response to nitrite / histidine kinase / phosphorelay sensor kinase activity / nitrate assimilation / protein dimerization activity / signal transduction / ATP binding / plasma membrane
Similarity search - Function
Signal transduction histidine kinase, nitrate/nitrite-sensing / NarX-like, N-terminal domain superfamily / NarX-like, N-terminal / Type IV pili methyl-accepting chemotaxis transducer N-term / Signal transduction histidine kinase, subgroup 3, dimerisation and phosphoacceptor domain / Histidine kinase / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain ...Signal transduction histidine kinase, nitrate/nitrite-sensing / NarX-like, N-terminal domain superfamily / NarX-like, N-terminal / Type IV pili methyl-accepting chemotaxis transducer N-term / Signal transduction histidine kinase, subgroup 3, dimerisation and phosphoacceptor domain / Histidine kinase / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Nitrate/nitrite sensor protein NarQ
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGushchin, I. / Melnikov, I. / Polovinkin, V. / Ishchenko, A. / Popov, A. / Gordeliy, V.
CitationJournal: Science / Year: 2017
Title: Mechanism of transmembrane signaling by sensor histidine kinases.
Authors: Gushchin, I. / Melnikov, I. / Polovinkin, V. / Ishchenko, A. / Yuzhakova, A. / Buslaev, P. / Bourenkov, G. / Grudinin, S. / Round, E. / Balandin, T. / Borshchevskiy, V. / Willbold, D. / ...Authors: Gushchin, I. / Melnikov, I. / Polovinkin, V. / Ishchenko, A. / Yuzhakova, A. / Buslaev, P. / Bourenkov, G. / Grudinin, S. / Round, E. / Balandin, T. / Borshchevskiy, V. / Willbold, D. / Leonard, G. / Buldt, G. / Popov, A. / Gordeliy, V.
History
DepositionApr 18, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nitrate/nitrite sensor protein NarQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3557
Polymers26,7851
Non-polymers5706
Water1,60389
1
A: Nitrate/nitrite sensor protein NarQ
hetero molecules

A: Nitrate/nitrite sensor protein NarQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,70914
Polymers53,5702
Non-polymers1,14012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y+1/2,z1
Buried area7910 Å2
ΔGint-124 kcal/mol
Surface area22420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.593, 59.366, 239.583
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-305-

PO4

21A-409-

HOH

31A-453-

HOH

41A-464-

HOH

51A-467-

HOH

-
Components

#1: Protein Nitrate/nitrite sensor protein NarQ


Mass: 26784.889 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: narQ, b2469, JW2453 / Production host: Escherichia coli (E. coli) / References: UniProt: P27896, histidine kinase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.63 Å3/Da / Density % sol: 53.21 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / Details: in meso lipidic cubic phase crystallization

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.9→47.64 Å / Num. obs: 22889 / % possible obs: 99.8 % / Redundancy: 6.42 % / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Net I/σ(I): 13.77
Reflection shellResolution: 1.9→2 Å / Redundancy: 6.72 % / Rmerge(I) obs: 1.23 / Mean I/σ(I) obs: 1.42 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IJI

5iji


Resolution: 1.9→47.64 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.923 / SU B: 6.548 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.162 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28498 1148 5 %RANDOM
Rwork0.23175 ---
obs0.23424 21742 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 50.078 Å2
Baniso -1Baniso -2Baniso -3
1-5.1 Å20 Å2-0 Å2
2--1.27 Å20 Å2
3----6.37 Å2
Refinement stepCycle: 1 / Resolution: 1.9→47.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1749 0 30 89 1868
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191824
X-RAY DIFFRACTIONr_bond_other_d0.0010.021753
X-RAY DIFFRACTIONr_angle_refined_deg1.0181.9732495
X-RAY DIFFRACTIONr_angle_other_deg0.63333991
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0415232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.45424.32474
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.81115294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.875158
X-RAY DIFFRACTIONr_chiral_restr0.0520.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022053
X-RAY DIFFRACTIONr_gen_planes_other00.02426
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.1514.874913
X-RAY DIFFRACTIONr_mcbond_other5.124.868912
X-RAY DIFFRACTIONr_mcangle_it7.3557.2681138
X-RAY DIFFRACTIONr_mcangle_other7.3547.2761139
X-RAY DIFFRACTIONr_scbond_it6.7275.338910
X-RAY DIFFRACTIONr_scbond_other6.4365.256884
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.5127.7141317
X-RAY DIFFRACTIONr_long_range_B_refined12.10340.3012251
X-RAY DIFFRACTIONr_long_range_B_other12.02740.0562218
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 69 -
Rwork0.436 1568 -
obs--99.88 %

+
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