[English] 日本語
Yorodumi
- PDB-4cti: Escherichia coli EnvZ histidine kinase catalytic part fused to Ar... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4cti
TitleEscherichia coli EnvZ histidine kinase catalytic part fused to Archaeoglobus fulgidus Af1503 HAMP domain
ComponentsOSMOLARITY SENSOR PROTEIN ENVZ, AF1503
KeywordsSIGNALING PROTEIN / TWO-COMPONENT SIGNAL TRANSDUCTION / TCST / DHP DOMAIN / CA DOMAIN / PHOSPHORYL TRANSFER / STUTTER
Function / homology
Function and homology information


response to osmotic stress / histidine kinase / phosphorelay signal transduction system / phosphoprotein phosphatase activity / phosphorelay sensor kinase activity / outer membrane-bounded periplasmic space / protein autophosphorylation / phosphorylation / signal transduction / protein homodimerization activity ...response to osmotic stress / histidine kinase / phosphorelay signal transduction system / phosphoprotein phosphatase activity / phosphorelay sensor kinase activity / outer membrane-bounded periplasmic space / protein autophosphorylation / phosphorylation / signal transduction / protein homodimerization activity / ATP binding / identical protein binding / membrane / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal ...Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / 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 / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HAMP domain-containing protein / Sensor histidine kinase EnvZ
Similarity search - Component
Biological speciesARCHAEOGLOBUS FULGIDUS (archaea)
ESCHERICHIA COLI K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.847 Å
AuthorsFerris, H.U. / Coles, M. / Lupas, A.N. / Hartmann, M.D.
CitationJournal: J.Struct.Biol. / Year: 2014
Title: Crystallographic Snapshot of the Escherichia Coli Envz Histidine Kinase in an Active Conformation.
Authors: Ferris, H.U. / Coles, M. / Lupas, A.N. / Hartmann, M.D.
History
DepositionMar 13, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 1.2Mar 15, 2017Group: Source and taxonomy
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: OSMOLARITY SENSOR PROTEIN ENVZ, AF1503
B: OSMOLARITY SENSOR PROTEIN ENVZ, AF1503
C: OSMOLARITY SENSOR PROTEIN ENVZ, AF1503
D: OSMOLARITY SENSOR PROTEIN ENVZ, AF1503


Theoretical massNumber of molelcules
Total (without water)120,8054
Polymers120,8054
Non-polymers00
Water00
1
C: OSMOLARITY SENSOR PROTEIN ENVZ, AF1503
D: OSMOLARITY SENSOR PROTEIN ENVZ, AF1503


Theoretical massNumber of molelcules
Total (without water)60,4032
Polymers60,4032
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-46.8 kcal/mol
Surface area21620 Å2
MethodPISA
2
A: OSMOLARITY SENSOR PROTEIN ENVZ, AF1503
B: OSMOLARITY SENSOR PROTEIN ENVZ, AF1503


Theoretical massNumber of molelcules
Total (without water)60,4032
Polymers60,4032
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-46 kcal/mol
Surface area22110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.060, 76.620, 97.370
Angle α, β, γ (deg.)90.00, 107.03, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
OSMOLARITY SENSOR PROTEIN ENVZ, AF1503 / HAMP-DHP-CA CHIMERA


Mass: 30201.268 Da / Num. of mol.: 4 / Fragment: RESIDUES 278-326,228-450 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea), (gene. exp.) ESCHERICHIA COLI K-12 (bacteria)
Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: O28769, UniProt: P0AEJ4, histidine kinase

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growDetails: 0.2 M LITHIUM ACETATE AND 20 %(W/V) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→38.8 Å / Num. obs: 23475 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.32 % / Biso Wilson estimate: 68.59 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.87
Reflection shellResolution: 2.85→3.02 Å / Redundancy: 3.23 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.09 / % possible all: 97.1

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZRV

3zrv


Resolution: 2.847→38.83 Å / SU ML: 0.41 / σ(F): 1.37 / Phase error: 31.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2765 1167 5 %
Rwork0.2577 --
obs0.2587 23460 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.847→38.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6389 0 0 0 6389
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026479
X-RAY DIFFRACTIONf_angle_d0.718784
X-RAY DIFFRACTIONf_dihedral_angle_d14.7532338
X-RAY DIFFRACTIONf_chiral_restr0.0481062
X-RAY DIFFRACTIONf_plane_restr0.0051139
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8466-2.97610.35931390.30982684X-RAY DIFFRACTION96
2.9761-3.1330.31371460.29482775X-RAY DIFFRACTION100
3.133-3.32920.30011470.27492801X-RAY DIFFRACTION100
3.3292-3.58610.29081480.25782799X-RAY DIFFRACTION100
3.5861-3.94660.29381460.25322778X-RAY DIFFRACTION100
3.9466-4.5170.26071460.2262779X-RAY DIFFRACTION99
4.517-5.6880.24841470.25242811X-RAY DIFFRACTION100
5.688-38.83380.26461480.26262866X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4379-0.10090.51394.7716-4.86139.2866-0.1751-0.06070.0259-0.0695-0.1889-0.170.5218-0.1380.35190.43230.00490.06990.5138-0.02330.49992.436-5.22224.2742
2-0.1931-0.71420.19222.6107-3.73664.8005-0.15160.01190.03120.5166-0.3255-0.6134-0.24170.21370.49340.9073-0.1014-0.10810.6070.07340.6447.94823.25798.9811
33.8874-3.13393.29754.1016-3.22213.8031-0.0857-0.24810.27790.0624-0.101-0.25220.0076-0.16860.26070.8684-0.0099-0.07430.5776-0.05810.695819.294611.494641.785
46.0296-4.92896.56593.9533-6.11757.45990.50340.35580.3033-0.7972-0.6368-0.23980.87340.40150.12721.06720.1287-0.15780.5718-0.02030.710919.77862.816234.8821
52.73083.69471.43876.65260.71452.51010.50290.7288-1.20460.6842-0.68471.6344-0.3205-1.12980.06661.03670.17330.0411.1071-0.19651.3828-20.6555-4.8249.1012
69.50110.203-1.79866.1083.86726.0256-0.20160.3528-0.2776-0.70911.0666-1.258-0.01821.3261-0.70520.6357-0.06640.06411.0722-0.17370.83922.4057-12.33160.3282
72.82-2.3967-4.23283.91792.52598.08080.4053-2.15680.8761.33780.589-0.0956-3.1490.111-0.52251.93080.0185-0.04771.2931-0.1221.74570.489910.863356.1782
85.13881.7556-1.74564.28252.27526.95870.18330.122-0.0314-0.2587-0.0282-0.8913-0.67010.8686-0.13551.01330.07790.13831.2423-0.01830.860835.134118.230829.1045
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESSEQ 1:395
2X-RAY DIFFRACTION2CHAIN B AND RESSEQ 1:395
3X-RAY DIFFRACTION3CHAIN C AND RESSEQ 1:395
4X-RAY DIFFRACTION4CHAIN D AND RESSEQ 1:395
5X-RAY DIFFRACTION5CHAIN A AND RESSEQ 396:999
6X-RAY DIFFRACTION6CHAIN B AND RESSEQ 396:999
7X-RAY DIFFRACTION7CHAIN C AND RESSEQ 396:999
8X-RAY DIFFRACTION8CHAIN D AND RESSEQ 396:999

+
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