[English] 日本語
Yorodumi
- PDB-6g20: Crystal structure of a fluorescence optimized bathy phytochrome P... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6g20
TitleCrystal structure of a fluorescence optimized bathy phytochrome PAiRFP2 derived from wild-type Agp2 in its functional Meta-F intermediate state.
ComponentsBacteriophytochrome protein
KeywordsFLUORESCENT PROTEIN / SIGNALING PROTEIN / PHYTOCHROME / BACTERIOPHYTOCHROME / BILIN CHROMOPHORE / PHOTOISOMERIZATION / SIGNAL TRANSDUCTION / META-F STATE / LIGHT ADAPTATION / BATHY PHYTOCHROME / PHOTOSENSORY CORE MODULE / OPTOGENETIC / FLOURESCENCE
Function / homology
Function and homology information


protein histidine kinase activity / detection of visible light / histidine kinase / phosphorelay signal transduction system / photoreceptor activity / regulation of DNA-templated transcription / ATP binding
Similarity search - Function
Bacteriophytochrome, CheY-like / Signal transduction histidine kinase, HWE region / HWE histidine kinase / HWE histidine kinase / Phytochrome / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region ...Bacteriophytochrome, CheY-like / Signal transduction histidine kinase, HWE region / HWE histidine kinase / HWE histidine kinase / 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. / PAS domain / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / PAS domain superfamily / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-EL5 / Chem-ETE / DI(HYDROXYETHYL)ETHER / histidine kinase
Similarity search - Component
Biological speciesAgrobacterium fabrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsSchmidt, A. / Sauthof, L. / Szczepek, M. / Scheerer, P.
Funding support Germany, 1items
OrganizationGrant numberCountry
SFB1078 Germany
CitationJournal: Nat Commun / Year: 2018
Title: Structural snapshot of a bacterial phytochrome in its functional intermediate state.
Authors: Schmidt, A. / Sauthof, L. / Szczepek, M. / Lopez, M.F. / Escobar, F.V. / Qureshi, B.M. / Michael, N. / Buhrke, D. / Stevens, T. / Kwiatkowski, D. / von Stetten, D. / Mroginski, M.A. / ...Authors: Schmidt, A. / Sauthof, L. / Szczepek, M. / Lopez, M.F. / Escobar, F.V. / Qureshi, B.M. / Michael, N. / Buhrke, D. / Stevens, T. / Kwiatkowski, D. / von Stetten, D. / Mroginski, M.A. / Krauss, N. / Lamparter, T. / Hildebrandt, P. / Scheerer, P.
History
DepositionMar 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 24, 2023Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bacteriophytochrome protein
B: Bacteriophytochrome protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,71436
Polymers113,3572
Non-polymers4,35734
Water5,603311
1
A: Bacteriophytochrome protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)353,100108
Polymers340,0726
Non-polymers13,028102
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation9_555-x,-x+y,-z1
Buried area48710 Å2
ΔGint-1036 kcal/mol
Surface area114330 Å2
MethodPISA
2
B: Bacteriophytochrome protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)353,184108
Polymers340,0726
Non-polymers13,113102
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
crystal symmetry operation10_554-y,-x,-z-1/21
crystal symmetry operation11_654-x+y+1,y,-z-1/21
crystal symmetry operation12_544x,x-y-1,-z-1/21
Buried area45600 Å2
ΔGint-922 kcal/mol
Surface area120800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.114, 183.114, 179.655
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-602-

SO4

21A-602-

SO4

31A-610-

SO4

41A-610-

SO4

51B-602-

SO4

61B-602-

SO4

71B-609-

SO4

81B-609-

SO4

91B-611-

SO4

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Bacteriophytochrome protein


Mass: 56678.590 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium fabrum (strain C58 / ATCC 33970) (bacteria)
Gene: SY94_2021 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A9CI81

-
Non-polymers , 8 types, 345 molecules

#2: Chemical ChemComp-EL5 / 3-[(2Z)-2-({3-(2-carboxyethyl)-5-[(E)-(4-ethenyl-3-methyl-5-oxo-1,5-dihydro-2H-pyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-2-yl}methylidene)-5-{(Z)-[(3E,4S)-3-ethylidene-4-methyl-5-oxopyrrolidin-2-ylidene]methyl}-4-methyl-2H-pyrrol-3-yl]propanoic acid / biliverdin, bound form at Pfr state


Mass: 584.662 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H36N4O6
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-ETE / 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL


Mass: 208.252 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H20O5
#8: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.03 Å3/Da / Density % sol: 69.5 %
Crystal growTemperature: 279 K / Method: vapor diffusion / Details: (NH4)2SO4, VAPOR DIFFUSION, TEMPERATURE 279K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.16→47.79 Å / Num. obs: 95000 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 0.999 / Rpim(I) all: 0.031 / Net I/σ(I): 18.3
Reflection shellResolution: 2.16→2.28 Å / Redundancy: 20 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 13679 / CC1/2: 0.672 / Rpim(I) all: 0.409 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G1Z

6g1z


Resolution: 2.16→158.58 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.941 / SU B: 12.027 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23225 4842 5.1 %RANDOM
Rwork0.20905 ---
obs0.2102 90118 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.886 Å2
Baniso -1Baniso -2Baniso -3
1-2.01 Å21.01 Å20 Å2
2--2.01 Å2-0 Å2
3----6.53 Å2
Refinement stepCycle: 1 / Resolution: 2.16→158.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7512 0 262 311 8085
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.028115
X-RAY DIFFRACTIONr_bond_other_d0.0150.0217726
X-RAY DIFFRACTIONr_angle_refined_deg1.4682.01411047
X-RAY DIFFRACTIONr_angle_other_deg0.8353.01617721
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.48951017
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.45722.486358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.358151318
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9681579
X-RAY DIFFRACTIONr_chiral_restr0.0710.21238
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219057
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021898
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4232.3963924
X-RAY DIFFRACTIONr_mcbond_other1.422.3953923
X-RAY DIFFRACTIONr_mcangle_it2.4273.5724906
X-RAY DIFFRACTIONr_mcangle_other2.4263.5744907
X-RAY DIFFRACTIONr_scbond_it1.8622.8164191
X-RAY DIFFRACTIONr_scbond_other1.8622.8174192
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0234.1096112
X-RAY DIFFRACTIONr_long_range_B_refined6.96119.8158940
X-RAY DIFFRACTIONr_long_range_B_other6.96119.8218941
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.16→2.216 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 364 -
Rwork0.299 6572 -
obs--100 %
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)
11.2992-0.521-0.36531.33760.80071.36130.11440.0986-0.0893-0.0408-0.0431-0.03110.04520.1318-0.07130.01940.0218-0.05510.038-0.00310.65617.27-39.036-28.044
20.4778-0.3271-0.49690.28660.3991.2387-0.0326-0.0023-0.06860.0058-0.00370.0999-0.0128-0.07060.03630.00810.0040.01350.008-0.01570.825456.561-49.697-32.852
30.1881-0.0338-0.19391.22490.45390.7872-0.0181-0.0491-0.0050.07980.09290.03990.06440.0082-0.07480.0336-0.0054-0.03750.04480.02070.7122-2.713-28.67912.074
400000000000000-00.6487000.648700.6487000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 306
2X-RAY DIFFRACTION2B5 - 306
3X-RAY DIFFRACTION3A307 - 506
4X-RAY DIFFRACTION4B307 - 507

+
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