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- PDB-5uyr: Crystal structure of the dark-adapted full-length bacteriophytoch... -

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Basic information

Entry
Database: PDB / ID: 5uyr
TitleCrystal structure of the dark-adapted full-length bacteriophytochrome XccBphP mutant D199A from Xanthomonas campestris
ComponentsBacteriophytochrome
KeywordsSIGNALING PROTEIN / biliverdin / phytochrome / red-light photoreceptor / signal transduction
Function / homology
Function and homology information


detection of visible light / photoreceptor activity / regulation of DNA-templated transcription
Similarity search - Function
: / PAS fold / Phytochrome / GAF domain / Phytochrome, PHY domain superfamily / Phytochrome, central region / PAS fold-2 / PAS fold / Phytochrome region / Phytochrome chromophore attachment domain ...: / PAS fold / Phytochrome / GAF domain / Phytochrome, PHY domain superfamily / Phytochrome, central region / PAS fold-2 / PAS fold / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / PAS domain / PAS domain / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BILIVERDINE IX ALPHA / Bacteriophytochrome
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 Å
AuthorsOtero, L.H. / Klinke, S. / Goldbaum, F.A. / Bonomi, H.R.
CitationJournal: Febs J. / Year: 2021
Title: Pr-favoured variants of the bacteriophytochrome from the plant pathogen Xanthomonas campestris hint on light regulation of virulence-associated mechanisms.
Authors: Conforte, V. / Otero, L.H. / Toum, L. / Sirigu, S. / Antelo, G.T. / Rinaldi, J. / Foscaldi, S. / Klinke, S. / Chavas, L.M.G. / Vojnov, A.A. / Goldbaum, F.A. / Malamud, F. / Bonomi, H.R.
History
DepositionFeb 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2018Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.2Nov 24, 2021Group: 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 1.3Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacteriophytochrome
B: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,6104
Polymers142,4442
Non-polymers1,1652
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9030 Å2
ΔGint-64 kcal/mol
Surface area52970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.860, 103.860, 342.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Bacteriophytochrome / BphP / XccBphP


Mass: 71222.156 Da / Num. of mol.: 2 / Mutation: D199A
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)pLysS / References: UniProt: A0A0H2XCS3
#2: Chemical ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H34N4O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
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: 3.21 Å3/Da / Density % sol: 61.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.9 / Details: 7%(W/V) PEG 4000 0.2 M SODIUM ACETATE 0.1 M TRIS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 11, 2016
Details: Convex prefocussing mirror and a Kirkpatrick-Baez pair of focussing mirrors
RadiationMonochromator: Cryogenically cooled channel cut Si[111] crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 3.45→48.94 Å / Num. obs: 25772 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 12.4 % / Biso Wilson estimate: 124.23 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.048 / Rsym value: 0.172 / Net I/σ(I): 10.6
Reflection shellResolution: 3.45→3.69 Å / Redundancy: 12 % / Rmerge(I) obs: 1.536 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4569 / CC1/2: 0.69 / Rpim(I) all: 0.459 / Rsym value: 1.605 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AKP

5akp


Resolution: 3.45→47.27 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.915 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.516
Details: Due to the low resolution, the initial refinement was done under LSSR restraints using the atomic coordinates from PDB:5AKP. The B-factors were refined as groups.
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1258 4.9 %RANDOM
Rwork0.23 ---
obs0.231 25682 100 %-
Displacement parametersBiso mean: 134.73 Å2
Baniso -1Baniso -2Baniso -3
1-1.6451 Å20 Å20 Å2
2--1.6451 Å20 Å2
3----3.2902 Å2
Refine analyzeLuzzati coordinate error obs: 0 Å
Refinement stepCycle: 1 / Resolution: 3.45→47.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9367 0 86 2 9455
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019674HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1913202HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4437SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes224HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1491HARMONIC5
X-RAY DIFFRACTIONt_it9674HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.71
X-RAY DIFFRACTIONt_other_torsion4.09
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1245SEMIHARMONIC5
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_contact11360SEMIHARMONIC4
LS refinement shellResolution: 3.45→3.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.304 132 4.65 %
Rwork0.282 2705 -
all0.283 2837 -
obs--99.93 %

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