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- PDB-6pl0: Crystal structure of the dark-adapted full-length bacteriophytoch... -

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Basic information

Entry
Database: PDB / ID: 6pl0
TitleCrystal structure of the dark-adapted full-length bacteriophytochrome XccBphP from Xanthomonas campestris in the Pr state bound to BV chromophore
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
PAS fold / 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 ...PAS fold / 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: 2.96 Å
AuthorsOtero, L.H. / Sirigu, S. / Klinke, S. / Goldbaum, F. / Chavas, L. / 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
DepositionJun 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 12, 2022Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: Bacteriophytochrome
B: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,6984
Polymers142,5322
Non-polymers1,1652
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9260 Å2
ΔGint-64 kcal/mol
Surface area52450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.530, 103.530, 346.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Bacteriophytochrome / BphP / XccBphP


Mass: 71266.172 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: C33H34N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.26 Å3/Da / Density % sol: 62.25 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 12%(W/V) PEG 4000, 0.1 M TRIS, 0.2 M SODIUM ACETATE PH 8.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.96→50 Å / Num. obs: 40526 / % possible obs: 99.6 % / Redundancy: 17.2 % / Biso Wilson estimate: 140.34 Å2 / CC1/2: 1 / Net I/σ(I): 15.6
Reflection shellResolution: 2.96→3.13 Å / Redundancy: 17.3 % / Mean I/σ(I) obs: 0.79 / Num. unique obs: 3937 / CC1/2: 0.391 / % possible all: 98

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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: 2.96→49.6 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / SU R Cruickshank DPI: 1.348 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.354 / SU Rfree Blow DPI: 0.351 / SU Rfree Cruickshank DPI: 0.357
RfactorNum. reflection% reflectionSelection details
Rfree0.248 2021 5 %RANDOM
Rwork0.206 ---
obs0.209 40407 100 %-
Displacement parametersBiso max: 249.96 Å2 / Biso mean: 121.08 Å2 / Biso min: 54.73 Å2
Baniso -1Baniso -2Baniso -3
1--5.586 Å20 Å20 Å2
2---5.586 Å20 Å2
3---11.1721 Å2
Refinement stepCycle: final / Resolution: 2.96→49.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9509 0 86 2 9597
Biso mean--129.75 122.51 -
Num. residues----1214
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4512SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes234HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1513HARMONIC5
X-RAY DIFFRACTIONt_it9837HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1264SEMIHARMONIC5
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_contact11103SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d9837HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg13429HARMONIC21.17
X-RAY DIFFRACTIONt_omega_torsion2.85
X-RAY DIFFRACTIONt_other_torsion3.99
LS refinement shellResolution: 2.96→3.04 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3467 146 5.02 %
Rwork0.2655 2764 -
all0.2695 2910 -
obs--99.69 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.54160.2531-0.19180.83360.35821.90040.0673-0.05170.0284-0.0324-0.08820.27580.2835-0.49510.021-0.1734-0.152-0.0562-0.23760.0376-0.0966-30.608237.1429-6.9455
21.0580.26691.12460.85050.73732.59420.107-0.0655-0.20740.11780.0707-0.15870.21090.2424-0.1777-0.2066-0.1135-0.0557-0.29270.1318-0.0961-7.22537.2921-8.8695
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A11 - 634
2X-RAY DIFFRACTION2{ B|* }B11 - 634

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