[English] 日本語
Yorodumi
- PDB-6exr: CHEMOTAXIS PROTEIN CHEY FROM Pyrococcus horikoshiI -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6exr
TitleCHEMOTAXIS PROTEIN CHEY FROM Pyrococcus horikoshiI
Components120aa long hypothetical chemotaxis protein (CheY)
KeywordsSIGNALING PROTEIN / SIGNAL TRANSDUCTION PROTEIN
Function / homologyphosphorelay signal transduction system / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / 120aa long hypothetical chemotaxis protein (CheY)
Function and homology information
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsPaithankar, K.S. / Enderle, M.E. / Wirthensohn, D. / Grininger, M. / Oesterhelt, D.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2019
Title: Structure of the archaeal chemotaxis protein CheY in a domain-swapped dimeric conformation.
Authors: Paithankar, K.S. / Enderle, M. / Wirthensohn, D.C. / Miller, A. / Schlesner, M. / Pfeiffer, F. / Rittner, A. / Grininger, M. / Oesterhelt, D.
History
DepositionNov 9, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 11, 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 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: 120aa long hypothetical chemotaxis protein (CheY)
B: 120aa long hypothetical chemotaxis protein (CheY)
C: 120aa long hypothetical chemotaxis protein (CheY)
D: 120aa long hypothetical chemotaxis protein (CheY)
E: 120aa long hypothetical chemotaxis protein (CheY)
F: 120aa long hypothetical chemotaxis protein (CheY)


Theoretical massNumber of molelcules
Total (without water)79,1446
Polymers79,1446
Non-polymers00
Water00
1
A: 120aa long hypothetical chemotaxis protein (CheY)
B: 120aa long hypothetical chemotaxis protein (CheY)
C: 120aa long hypothetical chemotaxis protein (CheY)
D: 120aa long hypothetical chemotaxis protein (CheY)
E: 120aa long hypothetical chemotaxis protein (CheY)
F: 120aa long hypothetical chemotaxis protein (CheY)

A: 120aa long hypothetical chemotaxis protein (CheY)
B: 120aa long hypothetical chemotaxis protein (CheY)
C: 120aa long hypothetical chemotaxis protein (CheY)
D: 120aa long hypothetical chemotaxis protein (CheY)
E: 120aa long hypothetical chemotaxis protein (CheY)
F: 120aa long hypothetical chemotaxis protein (CheY)


Theoretical massNumber of molelcules
Total (without water)158,28812
Polymers158,28812
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area35860 Å2
ΔGint-340 kcal/mol
Surface area64800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.140, 124.370, 73.420
Angle α, β, γ (deg.)90.000, 111.750, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Chains A B
21Chains A C
31Chains A D
41Chains A E
51Chains A F
61Chains B C
71Chains B D
81Chains B E
91Chains B F
101Chains C D
111Chains C E
121Chains C F
131Chains D E
141Chains D F
151Chains E F

-
Components

#1: Protein
120aa long hypothetical chemotaxis protein (CheY)


Mass: 13190.697 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: PH0482 / Production host: Escherichia coli (E. coli) / References: UniProt: O58193

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.93 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Tris-HCl, 1.2 M sodium malonate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.16→68.19 Å / Num. obs: 47836 / % possible obs: 98.2 % / Redundancy: 7.4 % / Biso Wilson estimate: 40.95 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.023 / Rrim(I) all: 0.062 / Net I/σ(I): 22.8
Reflection shellResolution: 2.16→2.2 Å / Redundancy: 5.7 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1953 / CC1/2: 0.56 / Rpim(I) all: 0.6 / Rrim(I) all: 1.6 / % possible all: 82

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158 2016/10/03refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1u0s

1u0s


Resolution: 2.16→68.193 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.25 / WRfactor Rwork: 0.222 / SU B: 7.515 / SU ML: 0.184 / Cross valid method: FREE R-VALUE / ESU R: 0.252 / ESU R Free: 0.208
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2751 2338 -
Rwork0.242 45497 -
all0.244 --
obs-47835 98.19 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 54.307 Å2
Baniso -1Baniso -2Baniso -3
1--0.263 Å20 Å21.163 Å2
2---0.561 Å2-0 Å2
3----0.078 Å2
Refinement stepCycle: LAST / Resolution: 2.16→68.193 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5344 0 0 0 5344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0195388
X-RAY DIFFRACTIONr_bond_other_d0.0020.025614
X-RAY DIFFRACTIONr_angle_refined_deg1.7921.9927218
X-RAY DIFFRACTIONr_angle_other_deg1.01313042
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0815690
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.78426.526190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.545151136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6761518
X-RAY DIFFRACTIONr_chiral_restr0.0990.2878
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025702
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02860
X-RAY DIFFRACTIONr_nbd_refined0.2250.21974
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1540.210156
X-RAY DIFFRACTIONr_nbtor_refined0.1650.25206
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.26024
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.262
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1240.226
X-RAY DIFFRACTIONr_nbd_other0.1960.2164
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0620.22
X-RAY DIFFRACTIONr_mcbond_it4.8245.0392784
X-RAY DIFFRACTIONr_mcbond_other4.8215.0392783
X-RAY DIFFRACTIONr_mcangle_it6.3717.5423466
X-RAY DIFFRACTIONr_mcangle_other6.377.5423467
X-RAY DIFFRACTIONr_scbond_it6.0675.7342604
X-RAY DIFFRACTIONr_scbond_other6.0665.7342605
X-RAY DIFFRACTIONr_scangle_it9.0048.2823752
X-RAY DIFFRACTIONr_scangle_other9.0038.2823753
X-RAY DIFFRACTIONr_lrange_it10.7359.6255605
X-RAY DIFFRACTIONr_lrange_other10.72959.6285606
X-RAY DIFFRACTIONr_ncsr_local_group_10.1020.056550
X-RAY DIFFRACTIONr_ncsr_local_group_20.0920.056552
X-RAY DIFFRACTIONr_ncsr_local_group_30.0880.056648
X-RAY DIFFRACTIONr_ncsr_local_group_40.1080.056478
X-RAY DIFFRACTIONr_ncsr_local_group_50.0660.056760
X-RAY DIFFRACTIONr_ncsr_local_group_60.1140.056438
X-RAY DIFFRACTIONr_ncsr_local_group_70.1030.056576
X-RAY DIFFRACTIONr_ncsr_local_group_80.1150.056422
X-RAY DIFFRACTIONr_ncsr_local_group_90.1030.056554
X-RAY DIFFRACTIONr_ncsr_local_group_100.1040.056518
X-RAY DIFFRACTIONr_ncsr_local_group_110.0930.056548
X-RAY DIFFRACTIONr_ncsr_local_group_120.0940.056530
X-RAY DIFFRACTIONr_ncsr_local_group_130.110.056476
X-RAY DIFFRACTIONr_ncsr_local_group_140.0970.056602
X-RAY DIFFRACTIONr_ncsr_local_group_150.1070.056486
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)WRfactor Rwork
2.16-2.2160.3771400.352818354883.37090.343
2.216-2.2770.4361590.3853107352492.67880.378
2.277-2.3430.4361710.3263221340299.70610.294
2.343-2.4150.3171590.2923154331499.96980.257
2.415-2.4940.3341540.2913035319699.7810.251
2.494-2.5810.3431490.299294230911000.254
2.581-2.6780.3521320.2792885301899.96690.234
2.678-2.7880.3121450.2582702284999.92980.218
2.788-2.9110.2821450.2712627277499.92790.235
2.911-3.0530.3721210.2762535265799.96240.248
3.053-3.2180.3081410.29236725081000.265
3.218-3.4130.3551270.272246237699.87370.254
3.413-3.6480.251110.2612139225299.91120.248
3.648-3.9390.286980.241199220901000.234
3.939-4.3140.221060.191181719231000.189
4.314-4.820.175770.1591669174799.94280.163
4.82-5.5610.217740.197145615301000.2
5.561-6.80.351530.22125813111000.221
6.8-9.5690.144450.165972102099.70590.177
9.569-68.1930.141310.2145555861000.235

+
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