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- PDB-9dza: Photoactivation in Bacteriophytochrome, high resolution cryo stru... -

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Basic information

Entry
Database: PDB / ID: 9dza
TitlePhotoactivation in Bacteriophytochrome, high resolution cryo structure in the dark.
ComponentsPhotoreceptor-histidine kinase BphP
KeywordsSIGNALING PROTEIN / bacteriophytochrome myxobacterial
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
Chem-EL5 / histidine kinase
Similarity search - Component
Biological speciesStigmatella aurantiaca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.4 Å
AuthorsMalla, T.N. / Stojkovic, E.A. / Schmidt, M.
Funding support United States, 3items
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
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
DepositionOct 15, 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

Downloads & links

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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)105,4595
Polymers103,9632
Non-polymers1,4963
Water22,1581230
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-26 kcal/mol
Surface area40040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.330, 81.690, 83.490
Angle α, β, γ (deg.)90.000, 107.070, 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-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-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1230 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.58 Å3/Da / Density % sol: 52.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: Hampton Crystal Screen, Cryo, HR2-122, #9 plus 3 % benzamidine HCl, 1:1 with protein, 30 mg/ml.

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 19, 2020
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.4→57 Å / Num. obs: 196338 / % possible obs: 93 % / Redundancy: 3.5 % / Biso Wilson estimate: 16.62 Å2 / CC1/2: 0.98 / Net I/σ(I): 4.4
Reflection shellResolution: 1.4→1.43 Å / Redundancy: 3.4 % / Num. unique obs: 32602 / CC1/2: 0.2 / % possible all: 93

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
MOSFLMdata reduction
Aimlessdata scaling
Cootmodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.4→56.68 Å / SU ML: 0.2393 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.7675
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2446 9603 5.02 %
Rwork0.1954 339058 -
obs0.1979 192078 87.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.73 Å2
Refinement stepCycle: LAST / Resolution: 1.4→56.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7322 0 108 1230 8660
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00537597
X-RAY DIFFRACTIONf_angle_d0.882510362
X-RAY DIFFRACTIONf_chiral_restr0.07271172
X-RAY DIFFRACTIONf_plane_restr0.00911360
X-RAY DIFFRACTIONf_dihedral_angle_d18.08782797
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.35476370.330411129X-RAY DIFFRACTION85.39
1.42-1.430.41156440.342410961X-RAY DIFFRACTION85.07
1.43-1.450.38215740.338310753X-RAY DIFFRACTION83.62
1.45-1.470.34795480.316410810X-RAY DIFFRACTION82.45
1.47-1.490.34755300.31019595X-RAY DIFFRACTION74.14
1.49-1.510.32756020.294411051X-RAY DIFFRACTION85.74
1.51-1.530.33596100.283911408X-RAY DIFFRACTION88.19
1.53-1.550.33485710.274711513X-RAY DIFFRACTION88.23
1.55-1.580.32116430.26711497X-RAY DIFFRACTION88.62
1.58-1.60.30177030.260511387X-RAY DIFFRACTION88.55
1.6-1.630.31546140.253311377X-RAY DIFFRACTION87.84
1.63-1.660.30795340.254411416X-RAY DIFFRACTION87.49
1.66-1.690.30065600.247511156X-RAY DIFFRACTION86.28
1.69-1.730.3086160.239610819X-RAY DIFFRACTION83.63
1.73-1.760.26555010.22639860X-RAY DIFFRACTION75.98
1.76-1.80.26595270.214311793X-RAY DIFFRACTION89.77
1.8-1.850.24625960.200811810X-RAY DIFFRACTION90.77
1.85-1.90.25595860.197611789X-RAY DIFFRACTION90.4
1.9-1.960.25276120.193611701X-RAY DIFFRACTION90.4
1.96-2.020.2486240.186111727X-RAY DIFFRACTION90.64
2.02-2.090.24646040.189811611X-RAY DIFFRACTION89.21
2.09-2.180.23725750.181610990X-RAY DIFFRACTION84.89
2.18-2.270.23065950.174910492X-RAY DIFFRACTION81
2.27-2.390.24796040.17912173X-RAY DIFFRACTION93.86
2.39-2.540.2375660.179312247X-RAY DIFFRACTION93.61
2.54-2.740.25086010.183112014X-RAY DIFFRACTION92.21
2.74-3.020.22616730.182211439X-RAY DIFFRACTION88.99
3.02-3.450.21835490.171810816X-RAY DIFFRACTION83.1
3.45-4.350.20427240.160212158X-RAY DIFFRACTION94.35
4.35-56.680.20255860.175611566X-RAY DIFFRACTION89

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