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- PDB-7jr5: Real Time Reaction Intermediates in Stigmatella Bacteriophytochrome P2 -

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Basic information

Entry
Database: PDB / ID: 7jr5
TitleReal Time Reaction Intermediates in Stigmatella Bacteriophytochrome P2
ComponentsPhotoreceptor-histidine kinase BphP
KeywordsSIGNALING PROTEIN / phytochrome / photosensory core domain / time-resolved serial femtosecond crystallography / nanosecond / red/far-red / Z to E isomerization
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 ...: / 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 / Histidine kinase-like ATPases / PAS domain superfamily / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
BENZAMIDINE / Chem-VHG / histidine kinase
Similarity search - Component
Biological speciesStigmatella aurantiaca (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsSchmidt, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) 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 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)106,9435
Polymers105,6452
Non-polymers1,2983
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-12 kcal/mol
Surface area44130 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


Mass: 52822.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stigmatella aurantiaca (strain DW4/3-1) (bacteria)
Strain: DW4/3-1 / Gene: STIAU_8420 / Production host: Escherichia coli (E. coli) / References: UniProt: Q09E27
#2: Chemical ChemComp-VHG / 3-[2-[[5-[(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1~{H}-pyrrol-2-yl]methyl]-5-[[(3~{S})-4-ethyl-3-methyl-2-oxidanylidene-1,3-dihydropyrrol-5-yl]methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid


Mass: 588.694 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H40N4O6 / 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.: 96 / 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: 2.76 Å3/Da / Density % sol: 55.42 %
Crystal growTemperature: 289 K / Method: batch mode / pH: 7
Details: SaBphP2 (60 mg/mL) was mixed 3:2 with a solution containing 0.17 M Ammonium-acetate, 85 mmol/L sodium citrate, pH 6.5, 25.5 % PEG 4000, 15% glycerol, 3 % benzamidine hydrochloride.

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Data collection

DiffractionMean temperature: 289 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, 2018
RadiationMonochromator: no / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.38 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 38486 / % possible obs: 100 % / Redundancy: 543 % / CC1/2: 0.96 / R split: 0.094 / Net I/σ(I): 15
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 158 % / Num. unique obs: 3035 / R split: 1.78 / % possible all: 100
Serial crystallography measurementFocal spot size: 5 µm2 / Pulse duration: 10 fsec. / Pulse photon energy: 8.9 keV / XFEL pulse repetition rate: 30 Hz
Serial crystallography sample deliveryDescription: viscous jet / Method: injection
Serial crystallography sample delivery injectionCarrier solvent: nuclear grade grease / Flow rate: 4 µL/min / Injector diameter: 100 µm / Injector temperature: 289 K / Jet diameter: 100 µm / Power by: HPLC / Preparation: folding with grease

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
CrystFELdata reduction
CrystFELdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6PTQ

6ptq


Resolution: 2.4→19.97 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.88 / SU B: 18.591 / SU ML: 0.407 / Cross valid method: THROUGHOUT / ESU R: 0.926 / ESU R Free: 0.403 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.34146 1799 4.7 %RANDOM
Rwork0.31275 ---
obs0.31412 36327 85.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.071 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å2-0 Å20.17 Å2
2---0.2 Å2-0 Å2
3----0.43 Å2
Refinement stepCycle: 1 / Resolution: 2.4→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7320 0 95 96 7511
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0137730
X-RAY DIFFRACTIONr_bond_other_d0.0020.0177352
X-RAY DIFFRACTIONr_angle_refined_deg2.2111.68310566
X-RAY DIFFRACTIONr_angle_other_deg1.2291.58916905
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.0595972
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.24919.95399
X-RAY DIFFRACTIONr_dihedral_angle_3_deg28.731151178
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5511580
X-RAY DIFFRACTIONr_chiral_restr0.2710.2944
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028784
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021660
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_it1.6892.5493876
X-RAY DIFFRACTIONr_mcbond_other1.6892.553875
X-RAY DIFFRACTIONr_mcangle_it2.6953.8244849
X-RAY DIFFRACTIONr_mcangle_other2.6953.8234850
X-RAY DIFFRACTIONr_scbond_it1.3152.6223854
X-RAY DIFFRACTIONr_scbond_other1.3152.6223855
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.13.915717
X-RAY DIFFRACTIONr_long_range_B_refined5.08631.3239457
X-RAY DIFFRACTIONr_long_range_B_other5.08431.3329453
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.585 99 -
Rwork0.464 2091 -
obs--67.26 %

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