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- PDB-9d2h: Stigmatella aurantica bacteriophytochrome protein 2 (SaBphP2), ph... -

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Basic information

Entry
Database: PDB / ID: 9d2h
TitleStigmatella aurantica bacteriophytochrome protein 2 (SaBphP2), photosensory core module, investigated at ESRF(EBS) ID29. Dark Structure.
Componentshistidine kinase
KeywordsSIGNALING PROTEIN / Photoreceptor Kinase / Myxobacterial Phytochrome / Photosensory Core Module.
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 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSchmidt, M. / Malla, T.N.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1231306 United States
National Science Foundation (NSF, United States)2423601 United States
CitationJournal: Iucrj / Year: 2025
Title: Exploiting fourth-generation synchrotron radiation for enzyme and photoreceptor characterization.
Authors: Malla, T.N. / Muniyappan, S. / Menendez, D. / Ogukwe, F. / Dale, A.N. / Clayton, J.D. / Weatherall, D.D. / Karki, P. / Dangi, S. / Mandella, V. / Pacheco, A.A. / Stojkovic, E.A. / Rose, S.L. ...Authors: Malla, T.N. / Muniyappan, S. / Menendez, D. / Ogukwe, F. / Dale, A.N. / Clayton, J.D. / Weatherall, D.D. / Karki, P. / Dangi, S. / Mandella, V. / Pacheco, A.A. / Stojkovic, E.A. / Rose, S.L. / Orlans, J. / Basu, S. / de Sanctis, D. / Schmidt, M.
History
DepositionAug 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)106,9305
Polymers105,6452
Non-polymers1,2853
Water6,864381
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-55 kcal/mol
Surface area42040 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 histidine kinase


Mass: 52822.488 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, histidine kinase
#2: Chemical ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H34N4O6
#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.: 381 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.73 Å3/Da / Density % sol: 55.03 %
Crystal growTemperature: 289 K / Method: batch mode / pH: 5.6
Details: 0.085 M Na-citrate, 25.5 % PEG 4000, 15 % glycerol, 3% benzamidine hydrochloride, pH 5.6. 2:3 protein/precipitant ratio

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.1 Å
DetectorType: PSI JUNGFRAU 4M / Detector: PIXEL / Date: Feb 12, 2023
RadiationMonochromator: multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.8→119 Å / Num. obs: 50696 / % possible obs: 100 % / Redundancy: 486 % / Biso Wilson estimate: 37.02 Å2 / CC1/2: 0.99 / R split: 0.096 / Net I/σ(I): 5
Reflection shellResolution: 2.1→2.15 Å / Num. unique obs: 3314 / CC1/2: 0.64 / R split: 9.9
Serial crystallography measurementSource size: 8 µm2
Serial crystallography sample deliveryDescription: chip / Method: fixed target
Serial crystallography sample delivery fixed targetDescription: chip scanning / Sample holding: mylar
Serial crystallography data reductionCrystal hits: 252933 / Lattices indexed: 83498

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→58.76 Å / SU ML: 0.4815 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 33.513
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2608 2447 4.83 %
Rwork0.1922 48247 -
obs0.1954 50694 76.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.63 Å2
Refinement stepCycle: LAST / Resolution: 2.1→58.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7320 0 95 381 7796
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01157593
X-RAY DIFFRACTIONf_angle_d1.080510362
X-RAY DIFFRACTIONf_chiral_restr0.0491172
X-RAY DIFFRACTIONf_plane_restr0.01641363
X-RAY DIFFRACTIONf_dihedral_angle_d16.22882812
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.140.4756990.44591954X-RAY DIFFRACTION52.45
2.14-2.190.4185860.41361863X-RAY DIFFRACTION50.1
2.19-2.240.426940.38352061X-RAY DIFFRACTION55.51
2.24-2.30.36741350.35652013X-RAY DIFFRACTION55.45
2.3-2.360.40261170.32962182X-RAY DIFFRACTION59.13
2.36-2.430.35341280.30892372X-RAY DIFFRACTION64.32
2.43-2.510.34331350.2912514X-RAY DIFFRACTION67.71
2.51-2.60.35831390.27222645X-RAY DIFFRACTION71.22
2.6-2.70.38461320.24962727X-RAY DIFFRACTION73.48
2.7-2.820.31951470.23872972X-RAY DIFFRACTION79.69
2.82-2.970.29111380.21643152X-RAY DIFFRACTION84.08
2.97-3.160.29891810.20393366X-RAY DIFFRACTION90.95
3.16-3.40.24851860.18433530X-RAY DIFFRACTION94.97
3.4-3.740.26111820.16223630X-RAY DIFFRACTION96.85
3.74-4.290.2151750.13893704X-RAY DIFFRACTION98.93
4.29-5.40.18321800.13823760X-RAY DIFFRACTION99.34
5.4-58.760.21831930.15533802X-RAY DIFFRACTION99.18

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