[English] 日本語
Yorodumi
- PDB-6t3u: PAS-GAF fragment from Deinococcus radiodurans phytochrome 1ps aft... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6t3u
TitlePAS-GAF fragment from Deinococcus radiodurans phytochrome 1ps after photoexcitation
ComponentsBacteriophytochrome
KeywordsTRANSFERASE / Kinase / Photosensor / Phytochrome
Function / homology
Function and homology information


osmosensory signaling via phosphorelay pathway / detection of visible light / phosphorelay response regulator activity / histidine kinase / phosphorelay sensor kinase activity / protein kinase activator activity / photoreceptor activity / regulation of DNA-templated transcription / ATP binding / identical protein binding
Similarity search - Function
: / 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. / Signal transduction histidine kinase-related protein, C-terminal ...: / 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. / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / PAS domain / 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 / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-LBV / Bacteriophytochrome
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsClaesson, E. / Takala, H. / Yuan Wahlgren, W. / Pandey, S. / Schmidt, M. / Westenhoff, S.
Funding support Sweden, Japan, Finland, 4items
OrganizationGrant numberCountry
European Research Council279944 Sweden
Japan Agency for Medical Research and Development (AMED) Japan
Academy of Finland285461 Finland
Academy of Finland296135 Finland
CitationJournal: Elife / Year: 2020
Title: The primary structural photoresponse of phytochrome proteins captured by a femtosecond X-ray laser.
Authors: Claesson, E. / Wahlgren, W.Y. / Takala, H. / Pandey, S. / Castillon, L. / Kuznetsova, V. / Henry, L. / Panman, M. / Carrillo, M. / Kubel, J. / Nanekar, R. / Isaksson, L. / Nimmrich, A. / ...Authors: Claesson, E. / Wahlgren, W.Y. / Takala, H. / Pandey, S. / Castillon, L. / Kuznetsova, V. / Henry, L. / Panman, M. / Carrillo, M. / Kubel, J. / Nanekar, R. / Isaksson, L. / Nimmrich, A. / Cellini, A. / Morozov, D. / Maj, M. / Kurttila, M. / Bosman, R. / Nango, E. / Tanaka, R. / Tanaka, T. / Fangjia, L. / Iwata, S. / Owada, S. / Moffat, K. / Groenhof, G. / A Stojkovic, E. / A Ihalainen, J. / Schmidt, M. / Westenhoff, S.
History
DepositionOct 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_related_exp_data_set
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.2Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Bacteriophytochrome
A: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,6304
Polymers74,4592
Non-polymers1,1712
Water2,648147
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-35 kcal/mol
Surface area26470 Å2
Unit cell
Length a, b, c (Å)54.980, 116.690, 117.860
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Bacteriophytochrome / Phytochrome-like protein


Mass: 37229.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Gene: bphP, DR_A0050 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9RZA4, histidine kinase
#2: Chemical ChemComp-LBV / 3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3- yl]propanoic acid / 2(R),3(E)- PHYTOCHROMOBILIN


Mass: 585.670 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H37N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.82 %
Crystal growTemperature: 298 K / Method: batch mode / pH: 4.95
Details: 60 mM Sodium Acetate, 3.3% PEG400, 1 mM DTT, 30% 2-methyl-2,4-pentanediol

-
Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.7712 Å
DetectorType: MPCCD / Detector: CCD / Date: Oct 12, 2018
RadiationMonochromator: graphite crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7712 Å / Relative weight: 1
ReflectionResolution: 2.21→41.46 Å / Num. obs: 39316 / % possible obs: 100 % / Redundancy: 106.11 % / CC1/2: 0.98 / R split: 0.1059 / Net I/σ(I): 6.1
Reflection shellResolution: 2.21→2.25 Å / Redundancy: 34.3 % / Mean I/σ(I) obs: 0.88 / Num. unique obs: 1512 / CC1/2: 0.38 / R split: 1.1464 / % possible all: 100
Serial crystallography sample deliveryDescription: grease jet / Method: injection
Serial crystallography sample delivery injectionCarrier solvent: Superlube

-
Processing

Software
NameVersionClassification
CrystFELdata reduction
CrystFEL0.6.3data scaling
PHASER2.5.7phasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K5B

5k5b


Resolution: 2.21→36.94 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.968 / SU B: 17.135 / SU ML: 0.358 / SU R Cruickshank DPI: 0.3423 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.342 / ESU R Free: 0.235
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2562 1829 5.2 %RANDOM
Rwork0.2304 ---
obs0.2317 33150 90.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 162.04 Å2 / Biso mean: 78.626 Å2 / Biso min: 42.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å2-0 Å2
2---0.99 Å2-0 Å2
3---1.32 Å2
Refinement stepCycle: final / Resolution: 2.21→36.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4794 0 86 147 5027
Biso mean--83.59 74.34 -
Num. residues----628
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0195136
X-RAY DIFFRACTIONr_bond_other_d0.0010.024921
X-RAY DIFFRACTIONr_angle_refined_deg1.15227056
X-RAY DIFFRACTIONr_angle_other_deg0.899311298
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8465648
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6823.255212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.06715760
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4541538
X-RAY DIFFRACTIONr_chiral_restr0.0610.2796
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215868
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021144
LS refinement shellResolution: 2.21→2.267 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.443 96 -
Rwork0.411 1787 -
all-1883 -
obs--67.18 %

+
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