[English] 日本語
Yorodumi
- PDB-5xub: The citrate-bound trimer of chemoreceptor MCP2201 ligand binding ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xub
TitleThe citrate-bound trimer of chemoreceptor MCP2201 ligand binding domain
ComponentsMethyl-accepting chemotaxis sensory transducer
KeywordsSIGNALING PROTEIN / methyl-accepting chemotaxis protein / four helix bundle / dicarboxylic organic acid binding
Function / homology
Function and homology information


chemotaxis / transmembrane signaling receptor activity / signal transduction / membrane
Similarity search - Function
: / Chemotaxis methyl-accepting receptor HlyB-like, 4HB MCP domain / Four helix bundle sensory module for signal transduction / Chemotaxis methyl-accepting receptor / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain ...: / Chemotaxis methyl-accepting receptor HlyB-like, 4HB MCP domain / Four helix bundle sensory module for signal transduction / Chemotaxis methyl-accepting receptor / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain
Similarity search - Domain/homology
CITRIC ACID / Methyl-accepting chemotaxis sensory transducer
Similarity search - Component
Biological speciesComamonas testosteroni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHong, Y. / Li, D.F. / Wang, D.C.
CitationJournal: Mol.Microbiol. / Year: 2019
Title: The ligand-binding domain of a chemoreceptor from Comamonas testosteroni has a previously unknown homotrimeric structure.
Authors: Hong, Y. / Huang, Z. / Guo, L. / Ni, B. / Jiang, C.Y. / Li, X.J. / Hou, Y.J. / Yang, W.S. / Wang, D.C. / Zhulin, I.B. / Liu, S.J. / Li, D.F.
History
DepositionJun 23, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / 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 1.2Nov 22, 2023Group: 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: Methyl-accepting chemotaxis sensory transducer
B: Methyl-accepting chemotaxis sensory transducer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6614
Polymers36,2772
Non-polymers3842
Water1,71195
1
A: Methyl-accepting chemotaxis sensory transducer
hetero molecules

A: Methyl-accepting chemotaxis sensory transducer
hetero molecules

A: Methyl-accepting chemotaxis sensory transducer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9926
Polymers54,4163
Non-polymers5763
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area3720 Å2
ΔGint-20 kcal/mol
Surface area22570 Å2
MethodPISA
2
B: Methyl-accepting chemotaxis sensory transducer
hetero molecules

B: Methyl-accepting chemotaxis sensory transducer
hetero molecules

B: Methyl-accepting chemotaxis sensory transducer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9926
Polymers54,4163
Non-polymers5763
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area3670 Å2
ΔGint-17 kcal/mol
Surface area22000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.400, 49.400, 406.342
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-421-

HOH

21A-440-

HOH

31B-435-

HOH

41B-446-

HOH

-
Components

#1: Protein Methyl-accepting chemotaxis sensory transducer


Mass: 18138.564 Da / Num. of mol.: 2 / Fragment: UNP residues 46-203
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Comamonas testosteroni (strain CNB-2) (bacteria)
Strain: CNB-2 / Gene: CtCNB1_2201 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: D0IVL9
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 53.24 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Sodium citrate pH 4.4, 14% PEG 400, 13% Ethylene glycol
PH range: 4.0 - 4.8

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.5→45.15 Å / Num. obs: 12095 / % possible obs: 94.5 % / Redundancy: 2.3 % / Biso Wilson estimate: 34.685 Å2 / CC1/2: 0.953 / Rmerge(I) obs: 0.152 / Net I/σ(I): 4.3
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1744 / CC1/2: 0.791 / % possible all: 94

-
Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
iMOSFLMdata processing
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XUD

5xud
PDB Unreleased entry


Resolution: 2.5→41.864 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 27.38
RfactorNum. reflection% reflectionSelection details
Rfree0.2567 1201 9.93 %Random
Rwork0.2034 ---
obs0.2087 12091 94.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→41.864 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2167 0 26 95 2288
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072209
X-RAY DIFFRACTIONf_angle_d0.9832990
X-RAY DIFFRACTIONf_dihedral_angle_d17.1061398
X-RAY DIFFRACTIONf_chiral_restr0.048365
X-RAY DIFFRACTIONf_plane_restr0.005384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.60020.29291380.24671215X-RAY DIFFRACTION94
2.6002-2.71850.32341320.23191211X-RAY DIFFRACTION95
2.7185-2.86180.27881300.23731209X-RAY DIFFRACTION95
2.8618-3.0410.29251340.22811211X-RAY DIFFRACTION94
3.041-3.27570.3331360.24381247X-RAY DIFFRACTION96
3.2757-3.60520.28271270.20621215X-RAY DIFFRACTION95
3.6052-4.12650.22661410.17111230X-RAY DIFFRACTION96
4.1265-5.19740.20951350.16641193X-RAY DIFFRACTION94
5.1974-41.86940.20181280.18761159X-RAY DIFFRACTION89
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)
10.82760.0479-0.49841.9374-1.81735.0252-0.0013-0.18830.22360.5815-0.17810.0077-0.5927-0.11750.15040.3502-0.0193-0.03130.2364-0.04740.42575.5702-7.668628.8585
21.45090.5309-0.78172.3894-3.78496.3021-0.0833-0.29140.22210.4861-0.56-0.9037-0.45611.00540.47250.3159-0.0067-0.08440.30250.0430.455114.6662-15.141328.2687
31.85180.5013-2.11021.4798-1.43854.76450.12640.37010.0106-0.1747-0.4896-0.72770.02230.70480.40280.2960.00440.14430.40050.15710.529814.7282-12.15318.3039
42.779-0.1253-1.07822.40380.09282.51550.1624-0.4460.32760.5229-0.023-0.3015-0.254-0.3714-0.22210.33850.0367-0.02330.3584-0.06430.18461.2259-20.943839.5358
51.8182-0.3616-2.78242.3017-2.05827.5923-0.22780.43470.0073-0.5059-0.11650.2683-0.1695-0.9345-0.1820.3086-0.0466-0.06050.3551-0.01430.436811.04653.6898-30.1455
62.2090.9873-2.3381.0177-1.69667.1173-0.25250.5482-0.3633-0.11530.2139-0.25090.4063-0.81310.270.2876-0.04980.04720.2912-0.03470.4057.6054-6.1027-24.6105
71.09851.3035-3.55441.649-2.87557.4679-0.544-0.104-0.6859-0.73580.02130.02821.40680.68310.38450.2911-0.02230.07380.331-0.03560.550120.4189-5.1378-27.0367
80.3630.2504-1.73244.0393-1.79999.0483-0.0813-1.3008-0.88010.5323-0.0386-0.12780.20721.44021.18680.23380.05640.00690.33090.33390.605317.8521-6.6828-7.0727
92.45970.115-0.13642.0663-1.36284.82540.28910.5183-0.2259-0.48610.04050.4049-0.38050.2683-0.35740.38420.0017-0.06070.303-0.05530.280919.32198.7435-36.3767
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 57 through 118 )
2X-RAY DIFFRACTION2chain 'A' and (resid 119 through 150 )
3X-RAY DIFFRACTION3chain 'A' and (resid 151 through 164 )
4X-RAY DIFFRACTION4chain 'A' and (resid 165 through 200 )
5X-RAY DIFFRACTION5chain 'B' and (resid 57 through 87 )
6X-RAY DIFFRACTION6chain 'B' and (resid 88 through 118 )
7X-RAY DIFFRACTION7chain 'B' and (resid 119 through 150 )
8X-RAY DIFFRACTION8chain 'B' and (resid 151 through 164 )
9X-RAY DIFFRACTION9chain 'B' and (resid 165 through 197 )

+
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