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- PDB-9md9: Photoactivation in Bacteriophytochromes; 3ps TR-SFX structure -

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Basic information

Entry
Database: PDB / ID: 9md9
TitlePhotoactivation in Bacteriophytochromes; 3ps TR-SFX structure
ComponentsPhotoreceptor-histidine kinase BphP
KeywordsSIGNALING PROTEIN / phytochrome / SaBphP2 / time-resolved serial femtosecond 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, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1231306 United States
National Science Foundation (NSF, United States)2423601 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 5, 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
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-52 kcal/mol
Surface area42910 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

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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: isolated from a natural source / Formula: C7H8N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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 % / Description: 15 - 20 micrometer plates
Crystal growTemperature: 293 K / Method: batch mode / pH: 5.6
Details: mother liquor: 0.17 M Ammonium-acetate, 0.085 M Sodium citrate pH 5.6, 25.5 % PEG 4000, 15% glycerol and 3 % Benzamidine protein:motherliquor 3:2
Temp details: room temperature

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Data collection

DiffractionMean temperature: 293 K / Ambient temp details: room temperature / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.3 Å
DetectorType: SLAC ePix10k 2M / Detector: PIXEL / Date: Feb 24, 2022
RadiationMonochromator: no monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 2.3→24.33 Å / Num. obs: 50738 / % possible obs: 100 % / Redundancy: 1262 % / CC1/2: 0.99 / R split: 0.083 / Net I/σ(I): 6.9
Reflection shellResolution: 2.3→2.34 Å / Mean I/σ(I) obs: 0.3 / Num. unique obs: 5024 / CC1/2: 0.164 / R split: 2.35 / % 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: 60 Hz
Serial crystallography sample deliveryDescription: viscous matrix / Method: injection
Serial crystallography sample delivery injectionCarrier solvent: nuclear grade grease (superlube) / Flow rate: 3 µL/min / Injector diameter: 75 µm / Preparation: mixing
Serial crystallography data reductionCrystal hits: 142564 / Frames indexed: 88398

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
CrystFEL0.9.1data reduction
CrystFEL0.9.1data scaling
PHENIX1.21refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.3→24.33 Å / SU ML: 0.5318 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 34.4246
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2956 1927 5.1 %
Rwork0.2239 35828 -
obs0.2276 37755 74.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.81 Å2
Refinement stepCycle: LAST / Resolution: 2.3→24.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7320 0 95 56 7471
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00817595
X-RAY DIFFRACTIONf_angle_d1.105710368
X-RAY DIFFRACTIONf_chiral_restr0.04931172
X-RAY DIFFRACTIONf_plane_restr0.01251365
X-RAY DIFFRACTIONf_dihedral_angle_d19.61952814
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.4967630.43151061X-RAY DIFFRACTION31.36
2.36-2.420.501830.40791420X-RAY DIFFRACTION42.27
2.42-2.490.5047950.39641643X-RAY DIFFRACTION48.22
2.49-2.570.44281120.3961754X-RAY DIFFRACTION51.8
2.57-2.670.4391170.36551993X-RAY DIFFRACTION58.59
2.67-2.770.39561410.34412315X-RAY DIFFRACTION68.26
2.77-2.90.41351480.32352626X-RAY DIFFRACTION76.97
2.9-3.050.40541400.30362873X-RAY DIFFRACTION83.83
3.05-3.240.30221640.23263138X-RAY DIFFRACTION91.17
3.24-3.490.28141840.19123285X-RAY DIFFRACTION95.86
3.49-3.840.24621580.17933379X-RAY DIFFRACTION98
3.84-4.40.20971570.15353425X-RAY DIFFRACTION98.7
4.4-5.530.20781900.14253440X-RAY DIFFRACTION99.59
5.53-24.330.20331750.15943476X-RAY DIFFRACTION98.54

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