[English] 日本語
Yorodumi
- PDB-6bay: Stigmatella aurantiaca bacterial phytochrome P1, PAS-GAF-PHY T289... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6bay
TitleStigmatella aurantiaca bacterial phytochrome P1, PAS-GAF-PHY T289H mutant, room temperature structure
ComponentsPhotoreceptor-histidine kinase BphP
KeywordsSIGNALING PROTEIN / bacterial phytochrome / Stigmatella aurantiaca / photosensory core module / PAS-GAF-PHY / room temperature / SACLA / T28H mutant
Function / homology
Function and homology information


detection of visible light / histidine kinase / phosphorelay sensor kinase activity / photoreceptor activity / regulation of DNA-templated transcription
Similarity search - Function
: / Phytochrome / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / GAF domain / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. ...: / Phytochrome / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / GAF domain / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / PAS domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / PAS domain superfamily / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-BLR / histidine kinase
Similarity search - Component
Biological speciesStigmatella aurantiaca DW4/3-1 (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsSchmidt, M. / Stojkovic, E.
Funding support United States, Finland, 7items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)STC-1231306 United States
National Science Foundation (NSF, United States)BIO-MCB 1413360 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T34 GM105549-01 NU-STARS United States
National Institutes of Health/National Eye Institute (NIH/NEI)EY024363 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM095583 United States
Academy of Finland296135 Finland
Academy of Finland285461 Finland
CitationJournal: IUCrJ / Year: 2018
Title: Structural basis for light control of cell development revealed by crystal structures of a myxobacterial phytochrome.
Authors: Woitowich, N.C. / Halavaty, A.S. / Waltz, P. / Kupitz, C. / Valera, J. / Tracy, G. / Gallagher, K.D. / Claesson, E. / Nakane, T. / Pandey, S. / Nelson, G. / Tanaka, R. / Nango, E. / ...Authors: Woitowich, N.C. / Halavaty, A.S. / Waltz, P. / Kupitz, C. / Valera, J. / Tracy, G. / Gallagher, K.D. / Claesson, E. / Nakane, T. / Pandey, S. / Nelson, G. / Tanaka, R. / Nango, E. / Mizohata, E. / Owada, S. / Tono, K. / Joti, Y. / Nugent, A.C. / Patel, H. / Mapara, A. / Hopkins, J. / Duong, P. / Bizhga, D. / Kovaleva, S.E. / St Peter, R. / Hernandez, C.N. / Ozarowski, W.B. / Roy-Chowdhuri, S. / Yang, J.H. / Edlund, P. / Takala, H. / Ihalainen, J. / Brayshaw, J. / Norwood, T. / Poudyal, I. / Fromme, P. / Spence, J.C.H. / Moffat, K. / Westenhoff, S. / Schmidt, M. / Stojkovic, E.A.
History
DepositionOct 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Photoreceptor-histidine kinase BphP
B: Photoreceptor-histidine kinase BphP
C: Photoreceptor-histidine kinase BphP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,3996
Polymers172,6453
Non-polymers1,7543
Water00
1
A: Photoreceptor-histidine kinase BphP
B: Photoreceptor-histidine kinase BphP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,2664
Polymers115,0962
Non-polymers1,1692
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-10 kcal/mol
Surface area45100 Å2
MethodPISA
2
C: Photoreceptor-histidine kinase BphP
hetero molecules

C: Photoreceptor-histidine kinase BphP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,2664
Polymers115,0962
Non-polymers1,1692
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area4910 Å2
ΔGint-14 kcal/mol
Surface area48100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.230, 84.230, 477.990
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Photoreceptor-histidine kinase BphP / Sensor protein


Mass: 57548.180 Da / Num. of mol.: 3 / Fragment: PAS-GAF-PHY (UNP residues 1-515) / Mutation: T289H
Source method: isolated from a genetically manipulated source
Details: Stigmatella aurantiaca bacterial phytochrome P1, SaBphP1-PCM-T289H mutant
Source: (gene. exp.) Stigmatella aurantiaca DW4/3-1 (bacteria)
Strain: DW4/3-1 / Gene: STAUR_8015, STIAU_3396 / Production host: Escherichia coli (E. coli) / References: UniProt: Q097N3
#2: Chemical ChemComp-BLR / 3-[5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-2-[[5-[(Z)-(3-ethenyl-4-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1H-pyrrol-2-yl]methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid / Bilirubin IX alpha


Mass: 584.662 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C33H36N4O6
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.62 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 11 mg/mL protein in 0.1 M MES, pH 6.2, 8-5% w/v PEG20000, 5.2% v/v acetonitrile

-
Data collection

DiffractionMean temperature: 293 K / Ambient temp details: room temperature in air, SACLA
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.3 Å
DetectorType: MPCCD / Detector: CCD / Date: Dec 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 3.15→53.8 Å / Num. obs: 52483 / % possible obs: 100 % / Redundancy: 399 % / CC1/2: 0.998 / Rmerge(I) obs: 0.0105 / Net I/σ(I): 4.76
Reflection shellResolution: 3.15→3.2 Å / Redundancy: 107 % / Num. unique obs: 1956 / CC1/2: 0.506 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6BAP

6bap


Resolution: 3.15→53.799 Å / SU ML: 0.65 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.03
RfactorNum. reflection% reflection
Rfree0.2819 1807 5 %
Rwork0.2215 --
obs0.2248 40760 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.15→53.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11905 0 129 0 12034
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01212325
X-RAY DIFFRACTIONf_angle_d1.59416732
X-RAY DIFFRACTIONf_dihedral_angle_d21.4777351
X-RAY DIFFRACTIONf_chiral_restr0.071796
X-RAY DIFFRACTIONf_plane_restr0.0092206
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0001-3.06990.4261210.38762435X-RAY DIFFRACTION97
3.0699-3.14660.40681250.36472549X-RAY DIFFRACTION100
3.1466-3.23170.36691300.33752564X-RAY DIFFRACTION100
3.2317-3.32680.381100.31832561X-RAY DIFFRACTION100
3.3268-3.43420.33431440.29862498X-RAY DIFFRACTION100
3.4342-3.55690.35561380.27932569X-RAY DIFFRACTION100
3.5569-3.69920.3491510.25882543X-RAY DIFFRACTION100
3.6992-3.86760.32811400.24022557X-RAY DIFFRACTION100
3.8676-4.07140.31231240.21882586X-RAY DIFFRACTION100
4.0714-4.32640.28681120.19532598X-RAY DIFFRACTION100
4.3264-4.66030.23531460.1862605X-RAY DIFFRACTION100
4.6603-5.12890.26551310.20362578X-RAY DIFFRACTION100
5.1289-5.87030.3191560.2292630X-RAY DIFFRACTION100
5.8703-7.39290.29461450.24532684X-RAY DIFFRACTION100
7.3929-53.80780.24041640.192766X-RAY DIFFRACTION97

+
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