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- PDB-9meb: Photoactivation in Bacteriophytochrome, 100 ps structure -

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Basic information

Entry
Database: PDB / ID: 9meb
TitlePhotoactivation in Bacteriophytochrome, 100 ps structure
ComponentsPhotoreceptor-histidine kinase BphP
KeywordsSIGNALING PROTEIN / Bacteriophytochrome / myxobacteria / time-resolved serial crystallography
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
Similarity search - Function
Phytochrome / : / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain ...Phytochrome / : / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / Signal transduction histidine kinase, dimerisation/phosphoacceptor 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 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
BENZAMIDINE / BILIVERDINE IX ALPHA / histidine kinase
Similarity search - Component
Biological speciesStigmatella aurantiaca (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsSchmidt, M. / Malla, T.
Funding support United States, European Union, 4items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1231306 United States
National Science Foundation (NSF, United States)2423601 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM105549 United States
European Research Council (ERC)279944European Union
CitationJournal: Commun Chem / Year: 2025
Title: Observation of early events in the photoactivation of Myxobacterial phytochrome using time-resolved serial femtosecond crystallography.
Authors: Malla, T.N. / Aldama, L. / Leon, V. / Feliz, D. / Hu, H. / Thomas, I. / Cellini, A. / Wahlgren, W.Y. / Nimmrich, A. / Botha, S. / Sierra, R. / Hunter, M.S. / Poitevin, F. / Lisova, S. / ...Authors: Malla, T.N. / Aldama, L. / Leon, V. / Feliz, D. / Hu, H. / Thomas, I. / Cellini, A. / Wahlgren, W.Y. / Nimmrich, A. / Botha, S. / Sierra, R. / Hunter, M.S. / Poitevin, F. / Lisova, S. / Batyuk, A. / Gate, G. / Jernigan, R. / Kupitz, C.J. / Maj, P. / Meszaros, P. / Kurttila, M. / Monrroy, L. / Luo, F. / Owada, S. / Kang, J. / Slavov, C. / Maj, M. / Gautier, C. / Kashipathy, M. / Tolstikova, A. / Mariani, V. / Barty, A. / Moss, F. / Schwander, P. / Liu, H. / Boutet, S. / Fromme, P. / Takala, H. / Ihalainen, J.A. / Weierstall, U. / Westenhoff, S. / Stojkovic, E.A. / Schmidt, M.
History
DepositionDec 6, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)105,2485
Polymers103,9632
Non-polymers1,2853
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6200 Å2
ΔGint-51 kcal/mol
Surface area42720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.690, 83.400, 86.870
Angle α, β, γ (deg.)90.000, 107.630, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Photoreceptor-histidine kinase BphP / PCM Myxobacterial Phytochrome


Mass: 51981.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stigmatella aurantiaca (bacteria) / Gene: STIAU_8420 / Production host: Escherichia coli (E. coli) / References: UniProt: Q09E27
#2: Chemical ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H34N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O
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: 2.78 Å3/Da / Density % sol: 55.74 %
Crystal growTemperature: 291 K / Method: batch mode / pH: 5.6
Details: mother liquor: 0.17 M Ammonium Acetate, 0.085 M Na-citrate, 25.5% PEG 4000, 15 % glycerol, 3 % benzamidine protein (60 mg/ml):mother liquor ratio: 2:3

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.3 Å
DetectorType: PSI JUNGFRAU 4M / Detector: PIXEL / Date: Feb 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 2.1→24.3 Å / Num. obs: 52117 / % possible obs: 100 % / Redundancy: 921 % / Biso Wilson estimate: 14.18 Å2 / CC1/2: 0.99 / R split: 0.095 / Net I/σ(I): 6.4
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 598 % / Num. unique obs: 6584 / CC1/2: 0.21 / R split: 2.08 / % possible all: 100
Serial crystallography measurementFocal spot size: 1.5 µm2 / Pulse duration: 40 fsec. / Pulse photon energy: 9.3 keV / XFEL pulse repetition rate: 120 Hz
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionCarrier solvent: Nuclear grade grease, Superlube / Description: viscous matrix injection / Flow rate: 3.5 µL/min / Injector diameter: 75 µm / Injector temperature: 293 K / Jet diameter: 100 µm / Preparation: mixing, folding
Serial crystallography data reductionCrystal hits: 93520 / Frames indexed: 59080

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
CrystFELv9.0.1data reduction
CrystFELv9.0.1data scaling
PHENIX1.21-4207refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.3→23.94 Å / SU ML: 0.4823 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 39.2381
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3558 2073 4.76 %
Rwork0.2708 41436 -
obs0.2748 43509 85.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.61 Å2
Refinement stepCycle: LAST / Resolution: 2.3→23.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7320 0 95 267 7682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00847645
X-RAY DIFFRACTIONf_angle_d1.189410442
X-RAY DIFFRACTIONf_chiral_restr0.05221173
X-RAY DIFFRACTIONf_plane_restr0.01431372
X-RAY DIFFRACTIONf_dihedral_angle_d20.89992844
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.350.41081140.34292039X-RAY DIFFRACTION64.58
2.35-2.410.43711150.35442123X-RAY DIFFRACTION65.94
2.41-2.480.42671070.35442300X-RAY DIFFRACTION72.04
2.48-2.550.42381260.33312511X-RAY DIFFRACTION78.72
2.55-2.630.42431310.33722557X-RAY DIFFRACTION79.41
2.63-2.730.49881340.33762700X-RAY DIFFRACTION84.3
2.73-2.840.42491400.33412814X-RAY DIFFRACTION88.39
2.84-2.960.38131240.31472913X-RAY DIFFRACTION89.64
2.96-3.120.43541720.30743009X-RAY DIFFRACTION94.34
3.12-3.320.41251640.31073107X-RAY DIFFRACTION97.44
3.32-3.570.39391520.2883166X-RAY DIFFRACTION98.08
3.57-3.930.35891290.24762619X-RAY DIFFRACTION81.09
3.93-4.490.27421470.20533069X-RAY DIFFRACTION94.78
4.49-5.650.22251590.19223248X-RAY DIFFRACTION99.56
5.65-23.940.23821590.17673261X-RAY DIFFRACTION98.42

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