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- PDB-6g1z: Crystal structure of a fluorescence optimized bathy phytochrome P... -

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Basic information

Entry
Database: PDB / ID: 6g1z
TitleCrystal structure of a fluorescence optimized bathy phytochrome PAiRFP2 derived from wild-type Agp2 in its Pfr state.
ComponentsBacteriophytochrome protein
KeywordsFLUORESCENT PROTEIN / SIGNALING PROTEIN / PHYTOCHROME / BACTERIOPHYTOCHROME / BILIN CHROMOPHORE / PHOTOISOMERIZATION / SIGNAL TRANSDUCTION / PFR-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: 2.03 Å
AuthorsSauthof, L. / Schmidt, A. / 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 1.2Oct 9, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.3May 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 1.4Feb 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 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)117,26530
Polymers113,3572
Non-polymers3,90828
Water15,367853
1
A: Bacteriophytochrome protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,33812
Polymers56,6791
Non-polymers1,66011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bacteriophytochrome protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,92718
Polymers56,6791
Non-polymers2,24817
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)182.377, 182.377, 179.883
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-605-

SO4

21A-605-

SO4

31B-602-

SO4

41B-602-

SO4

51B-608-

SO4

61B-608-

SO4

71B-612-

GOL

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Components

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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, histidine kinase

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Non-polymers , 7 types, 881 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.: 14 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: 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
#7: 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
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 853 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.81 Å3/Da / Density % sol: 67.71 %
Crystal growTemperature: 279 K / Method: vapor diffusion / Details: (NH4)2SO4, VAPOR DIFFUSION, TEMPERATURE 279K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2016 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR - SI-111 CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.03→47.73 Å / Num. obs: 113144 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 0.999 / Rpim(I) all: 0.04 / Net I/σ(I): 15.4
Reflection shellResolution: 2.03→2.14 Å / Redundancy: 13.6 % / Mean I/σ(I) obs: 1.9 / CC1/2: 0.592 / Rpim(I) all: 0.417 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALAdata scaling
PHASERphasing
REFMAC5.8.0135refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G1Y

6g1y


Resolution: 2.03→47.73 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.97 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.126 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.213 5579 4.9 %RANDOM
Rwork0.18 ---
obs0.182 107549 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.72 Å2-0.36 Å20 Å2
2---0.72 Å20 Å2
3---2.32 Å2
Refinement stepCycle: LAST / Resolution: 2.03→47.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7582 0 244 853 8679
Refine LS restraintsType: r_bond_refined_d / Dev ideal: 0.013 / Dev ideal target: 0.02 / Number: 8184
LS refinement shellResolution: 2.03→2.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 431 -
Rwork0.288 7838 -
obs--100 %

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