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- PDB-7l59: Crystal structure of the dark-adapted full-length bacteriophytoch... -

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Basic information

Entry
Database: PDB / ID: 7l59
TitleCrystal structure of the dark-adapted full-length bacteriophytochrome XccBphP-G454E variant from Xanthomonas campestris in the Pfr state
ComponentsBacteriophytochrome
KeywordsSIGNALING PROTEIN / Photoreceptor / Bacterial protein / Photosensor / Red/far-red light / Phytochrome / Signal transduction / Phytopathogen
Function / homology
Function and homology information


detection of visible light / 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. / PAS domain / GAF 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. / PAS domain / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily
Similarity search - Domain/homology
BILIVERDINE IX ALPHA / Bacteriophytochrome
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsOtero, L.H. / Antelo, G. / Sanchez-Lamas, M. / Klinke, S. / Goldbaum, F.A. / Rinaldi, J. / Bonomi, H.R.
Funding support Argentina, 2items
OrganizationGrant numberCountry
National Research Council (NRC, Argentina)PICT 2015-0621 Argentina
National Research Council (NRC, Argentina)PICT 2016-1425 Argentina
CitationJournal: Sci Adv / Year: 2021
Title: Structural basis for the Pr-Pfr long-range signaling mechanism of a full-length bacterial phytochrome at the atomic level.
Authors: Otero, L.H. / Foscaldi, S. / Antelo, G.T. / Rosano, G.L. / Sirigu, S. / Klinke, S. / Defelipe, L.A. / Sanchez-Lamas, M. / Battocchio, G. / Conforte, V. / Vojnov, A.A. / Chavas, L.M.G. / ...Authors: Otero, L.H. / Foscaldi, S. / Antelo, G.T. / Rosano, G.L. / Sirigu, S. / Klinke, S. / Defelipe, L.A. / Sanchez-Lamas, M. / Battocchio, G. / Conforte, V. / Vojnov, A.A. / Chavas, L.M.G. / Goldbaum, F.A. / Mroginski, M.A. / Rinaldi, J. / Bonomi, H.R.
History
DepositionDec 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9212
Polymers71,3381
Non-polymers5831
Water90150
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration, This assembly was evidenced by size-exclusion chromatography (SEC) coupled to static-light scattering (SLS) experiments
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)182.035, 182.035, 40.059
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Bacteriophytochrome / BphP / XccBphP


Mass: 71338.234 Da / Num. of mol.: 1 / Mutation: G454E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (strain 8004) (bacteria)
Strain: 8004 / Gene: bphP, XC_4241 / Plasmid: pET-24a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H2XCS3
#2: Chemical ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H34N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.39 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 30% (w/v) pentaerythritol propoxylate (5/4 PO/OH), 0.1 M MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.68→45.51 Å / Num. obs: 18944 / % possible obs: 100 % / Redundancy: 15.3 % / Biso Wilson estimate: 107.12 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.025 / Rrim(I) all: 0.1 / Net I/σ(I): 15.9
Reflection shellResolution: 2.68→2.81 Å / Redundancy: 15.5 % / Rmerge(I) obs: 1.431 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2464 / CC1/2: 0.771 / Rpim(I) all: 0.374 / Rrim(I) all: 1.479 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AKP

5akp


Resolution: 2.68→45.51 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.31
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1019 5.38 %RANDOM
Rwork0.196 ---
obs0.198 18941 100 %-
Displacement parametersBiso mean: 105.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.4011 Å20 Å20 Å2
2--0.4011 Å20 Å2
3----0.8021 Å2
Refinement stepCycle: 1 / Resolution: 2.68→45.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4713 0 43 51 4807
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014864HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.196635HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2234SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes117HARMONIC2
X-RAY DIFFRACTIONt_gen_planes711HARMONIC5
X-RAY DIFFRACTIONt_it4864HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.86
X-RAY DIFFRACTIONt_other_torsion3.46
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion627SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5465SEMIHARMONIC4
LS refinement shellResolution: 2.68→2.83 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3322 195 7.19 %
Rwork0.2681 2518 -
all0.2728 2713 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 22.6414 Å / Origin y: -9.9901 Å / Origin z: 15.6966 Å
111213212223313233
T-0.304 Å2-0.0432 Å20.0303 Å2--0.0874 Å2-0.045 Å2---0.21 Å2
L0.7458 °20.1682 °20.2174 °2-2.8483 °21.0929 °2--1.5674 °2
S0.0895 Å °-0.1942 Å °0.1922 Å °0.0539 Å °0.0319 Å °-0.2419 Å °-0.0338 Å °0.1312 Å °-0.1214 Å °
Refinement TLS groupSelection details: { A|* }

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