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Basic information

Entry
Database: PDB / ID: 7jri
TitleHigh-resolution Crystal Structures of Transient Intermediates in the Phytochrome Photocycle, 33 ms structure
ComponentsPhotoreceptor-histidine kinase BphP
KeywordsSIGNALING PROTEIN / light perception / red light receptor
Function / homology
Function and homology information


detection of visible light / histidine kinase / phosphorelay sensor kinase 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 / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily ...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
Chem-3Q8 / BENZAMIDINE / histidine kinase
Similarity search - Component
Biological speciesStigmatella aurantiaca (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSchmidt, M. / Stojkovic, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)NSF-1231306 United States
CitationJournal: Structure / Year: 2021
Title: High-resolution crystal structures of transient intermediates in the phytochrome photocycle.
Authors: Carrillo, M. / Pandey, S. / Sanchez, J. / Noda, M. / Poudyal, I. / Aldama, L. / Malla, T.N. / Claesson, E. / Wahlgren, W.Y. / Feliz, D. / Srajer, V. / Maj, M. / Castillon, L. / Iwata, S. / ...Authors: Carrillo, M. / Pandey, S. / Sanchez, J. / Noda, M. / Poudyal, I. / Aldama, L. / Malla, T.N. / Claesson, E. / Wahlgren, W.Y. / Feliz, D. / Srajer, V. / Maj, M. / Castillon, L. / Iwata, S. / Nango, E. / Tanaka, R. / Tanaka, T. / Fangjia, L. / Tono, K. / Owada, S. / Westenhoff, S. / Stojkovic, E.A. / Schmidt, M.
History
DepositionAug 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)105,2615
Polymers103,9632
Non-polymers1,2983
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-10 kcal/mol
Surface area43770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.690, 83.400, 86.870
Angle α, β, γ (deg.)90.00, 107.63, 90.00
Int Tables number4
Space group name H-MP1211

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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) / Strain: DW4/3-1 / Gene: STIAU_8420
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q09E27
#2: Chemical ChemComp-3Q8 / 3-[2-[[5-[[(3E,4S)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrol-2-yl]methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1H-pyrrol-2-yl]methyl]-5-[(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid


Mass: 588.694 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BEN / BENZAMIDINE / Benzamidine


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


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 41817

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.23 % / Description: plates (5 x 5 x 10 um**3)
Crystal growTemperature: 293 K / Method: batch mode
Details: 0.17 M Ammonium acetate, 0.085 M Sodium citrate tribasic dihydrate pH 5.6, 25.5% w/v Polyethylene glycol 4000, 15% v/v Glycerol (cryo-screen solution) and 3 % w/v Benzamidine Hydrochloride ...Details: 0.17 M Ammonium acetate, 0.085 M Sodium citrate tribasic dihydrate pH 5.6, 25.5% w/v Polyethylene glycol 4000, 15% v/v Glycerol (cryo-screen solution) and 3 % w/v Benzamidine Hydrochloride mixed with 60 mg/mL protein (3:2) protein to mother liquor ratio

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.38 Å
DetectorType: MPCCD / Detector: CCD / Date: Jun 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.38 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. obs: 68919 / % possible obs: 100 % / Redundancy: 449.4 % / CC1/2: 0.994 / R split: 0.094 / Net I/σ(I): 7.6
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 203 % / Num. unique obs: 2561 / CC1/2: 0.31 / R split: 1.12 / % possible all: 100
Serial crystallography measurementPulse duration: 10 fsec.
Serial crystallography sample deliveryDescription: Folded in Nuclear Grade Grease / Method: injection
Serial crystallography sample delivery injectionCarrier solvent: nuclear grade grease / Crystal conc.: 1000 / Description: viscous jet extrusion / Flow rate: 4 µL/min / Injector diameter: 100 µm / Injector temperature: 293 K / Jet diameter: 100 µm / Power by: HPLC / Preparation: crytals folded in viscous medium
Serial crystallography data reductionCrystal hits: 89389 / Frames indexed: 41817

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
CrystFELdata reduction
CrystFELdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PTQ

6ptq


Resolution: 2.4→24.33 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.884 / SU B: 16.929 / SU ML: 0.37 / Cross valid method: THROUGHOUT / ESU R: 0.86 / ESU R Free: 0.393 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33349 1792 4.7 %RANDOM
Rwork0.29241 ---
obs0.29435 36457 85.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.116 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20 Å20.32 Å2
2---0.57 Å2-0 Å2
3----0.36 Å2
Refinement stepCycle: 1 / Resolution: 2.4→24.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7320 0 95 99 7514
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0137739
X-RAY DIFFRACTIONr_bond_other_d0.0020.0177364
X-RAY DIFFRACTIONr_angle_refined_deg2.121.6810575
X-RAY DIFFRACTIONr_angle_other_deg1.2331.5916932
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.2775971
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.7319.95400
X-RAY DIFFRACTIONr_dihedral_angle_3_deg28.073151179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2991580
X-RAY DIFFRACTIONr_chiral_restr0.210.2945
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028783
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021661
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_it1.872.3213878
X-RAY DIFFRACTIONr_mcbond_other1.8682.3213877
X-RAY DIFFRACTIONr_mcangle_it3.0673.4784848
X-RAY DIFFRACTIONr_mcangle_other3.0673.4794849
X-RAY DIFFRACTIONr_scbond_it1.4192.4133861
X-RAY DIFFRACTIONr_scbond_other1.4192.4143862
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3933.5795727
X-RAY DIFFRACTIONr_long_range_B_refined6.11528.3499272
X-RAY DIFFRACTIONr_long_range_B_other6.11828.3769264
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.577 103 -
Rwork0.451 2131 -
obs--68.3 %

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