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- PDB-8rjm: Serial femtosecond X-ray structure of a fluorescence optimized ba... -

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Basic information

Entry
Database: PDB / ID: 8rjm
TitleSerial femtosecond X-ray structure of a fluorescence optimized bathy phytochrome PAiRFP2 derived from wild-type Agp2 in its Pfr state (I0a).
Componentshistidine kinase
KeywordsSIGNALING PROTEIN / fluorescent protein / phytochrome / bacteriophytochrome / Pfr-state / optogenetic
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 / Phytochrome, central region / PAS fold-2 / PAS fold / Phytochrome region ...Bacteriophytochrome, CheY-like / Signal transduction histidine kinase, HWE region / HWE histidine kinase / HWE histidine kinase / Phytochrome / Phytochrome, PHY domain superfamily / Phytochrome, central region / PAS fold-2 / PAS fold / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / 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 / PAS domain superfamily / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
Chem-EL5 / histidine kinase
Similarity search - Component
Biological speciesAgrobacterium fabrum str. C58 (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsSauthof, L. / Schmidt, A. / Szczepek, M. / Brewster, A.S. / Kern, J.F. / Scheerer, P.
Funding support Germany, Israel, United States, United Kingdom, 9items
OrganizationGrant numberCountry
German Research Foundation (DFG)CRC1078 - project number 221545957 Germany
German Research Foundation (DFG)CRC1423 - project number 421152132 Germany
German Research Foundation (DFG)EXC2008/1-390540038 Germany
Boehringer Ingelheim Fonds (BIF)BIF Travel Grant Germany
Israel Science Foundation3131/20 Israel
Department of Energy (DOE, United States)DE-AC02-76SF00515, DE-AC02-05CH11231 United States
National Institutes of Health/Office of the DirectorGM05530, GM110501, GM126289, GM117126, S10 OD023453 United States
Wellcome Trust210734/Z/18/Z United Kingdom
Royal SocietyRSWF- R2 - 182017 United Kingdom
CitationJournal: Sci Adv / Year: 2025
Title: Serial-femtosecond crystallography reveals how a phytochrome variant couples chromophore and protein structural changes.
Authors: Sauthof, L. / Szczepek, M. / Schmidt, A. / Bhowmick, A. / Dasgupta, M. / Mackintosh, M.J. / Gul, S. / Fuller, F.D. / Chatterjee, R. / Young, I.D. / Michael, N. / Heyder, N.A. / Bauer, B. / ...Authors: Sauthof, L. / Szczepek, M. / Schmidt, A. / Bhowmick, A. / Dasgupta, M. / Mackintosh, M.J. / Gul, S. / Fuller, F.D. / Chatterjee, R. / Young, I.D. / Michael, N. / Heyder, N.A. / Bauer, B. / Koch, A. / Bogacz, I. / Kim, I.S. / Simon, P.S. / Butryn, A. / Aller, P. / Chukhutsina, V.U. / Baxter, J.M. / Hutchison, C.D.M. / Liebschner, D. / Poon, B. / Sauter, N.K. / Miller, M.D. / Alonso-Mori, R. / Hunter, M.S. / Batyuk, A. / Owada, S. / Tono, K. / Tanaka, R. / van Thor, J.J. / Krauss, N. / Lamparter, T. / Brewster, A.S. / Schapiro, I. / Orville, A.M. / Yachandra, V.K. / Yano, J. / Hildebrandt, P. / Kern, J.F. / Scheerer, P.
History
DepositionDec 21, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2025Group: 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_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: histidine kinase
B: histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,71213
Polymers115,0152
Non-polymers1,69711
Water5,477304
1
A: histidine kinase
hetero molecules

A: histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,71314
Polymers115,0152
Non-polymers1,69812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area4370 Å2
ΔGint-45 kcal/mol
Surface area41520 Å2
MethodPISA
2
B: histidine kinase
hetero molecules

B: histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,71012
Polymers115,0152
Non-polymers1,69510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/21
Buried area3860 Å2
ΔGint-62 kcal/mol
Surface area42160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.980, 184.980, 182.538
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

31B-602-

SO4

41B-602-

SO4

51B-701-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein histidine kinase


Mass: 57507.484 Da / Num. of mol.: 2
Mutation: K69R, R83K, G120D, A123T, M163L, Q168E, R220P, S243N, V244F, G269D, A276V, Y270C, E294A, H303F, H333R, I336L, D349R, M351I, A386V, G409D, L419I, T469S, A487T, E494G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium fabrum str. C58 (bacteria)
Gene: Atu2165 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A9CI81, histidine kinase

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Non-polymers , 5 types, 315 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.98 Å3/Da / Density % sol: 69.07 %
Crystal growTemperature: 279 K / Method: batch mode
Details: 1.0 - 2.2 M ammonium sulphate, 2 - 12% PEG 1000, 0.1 M HEPES pH 6.8 - 7.7, 0.025% low-melt agarose

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.30129 Å
DetectorType: RAYONIX MX170-HS / Detector: CCD / Date: May 5, 2018 / Details: Compound refractive lenses
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.30129 Å / Relative weight: 1
ReflectionResolution: 2.15→25.75 Å / Num. obs: 99757 / % possible obs: 99.9 % / Redundancy: 309 % / CC1/2: 0.897 / Net I/σ(I): 39
Reflection shellResolution: 2.15→2.21 Å / Num. unique obs: 7086 / CC1/2: 0.079

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata scaling
DIALSdata reduction
PRIMEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→25.75 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.966 / SU B: 6.801 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21688 1998 2 %RANDOM
Rwork0.20382 ---
obs0.20408 97536 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.294 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å2-0.25 Å2-0 Å2
2---0.5 Å20 Å2
3---1.63 Å2
Refinement stepCycle: 1 / Resolution: 2.15→25.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7469 0 110 304 7883
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0137858
X-RAY DIFFRACTIONr_bond_other_d0.0050.0157329
X-RAY DIFFRACTIONr_angle_refined_deg1.2251.63810719
X-RAY DIFFRACTIONr_angle_other_deg1.1371.57216808
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4125998
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.03520.142423
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.208151228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4661565
X-RAY DIFFRACTIONr_chiral_restr0.040.21034
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028959
X-RAY DIFFRACTIONr_gen_planes_other0.0120.021835
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_it1.7636.133930
X-RAY DIFFRACTIONr_mcbond_other1.7636.1293929
X-RAY DIFFRACTIONr_mcangle_it3.0229.1794912
X-RAY DIFFRACTIONr_mcangle_other3.0229.184913
X-RAY DIFFRACTIONr_scbond_it1.8646.2973928
X-RAY DIFFRACTIONr_scbond_other1.8646.2983929
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2799.3715795
X-RAY DIFFRACTIONr_long_range_B_refined5.25869.5128310
X-RAY DIFFRACTIONr_long_range_B_other5.25769.5168311
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.444 145 -
Rwork0.411 7086 -
obs--99.61 %

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