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

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Basic information

Entry
Database: PDB / ID: 6ndo
TitleCrystal structure of the dark-adapted full-length bacteriophytochrome XccBphP mutant L193N from Xanthomonas campestris
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. / GAF 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. / GAF domain / 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: 3.58 Å
AuthorsOtero, L.H. / Sirigu, S. / Klinke, S. / Rinaldi, J. / Conforte, V. / Malamud, F. / Goldbaum, F.A. / Chavas, L. / Bonomi, H.R.
Funding support Argentina, 1items
OrganizationGrant numberCountry
National Agency for the Promotion of Science and Technology of Argentina (ANPCyT)PICT 2016-1425 Argentina
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
DepositionDec 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2020Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rsym_value / _reflns_shell.pdbx_Rsym_value
Revision 1.2Jun 30, 2021Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id
Revision 1.3Nov 24, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 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

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Assembly

Deposited unit
A: Bacteriophytochrome
B: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,7004
Polymers142,5342
Non-polymers1,1652
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8920 Å2
ΔGint-60 kcal/mol
Surface area52370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.600, 103.600, 343.690
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: 71267.109 Da / Num. of mol.: 2 / Mutation: L193N
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: isolated from a natural source / Formula: C33H34N4O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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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: 3.24 Å3/Da / Density % sol: 61.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 11 % (w/v) PEG 4000, 100 mM Hepes pH 7.5, 200 mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 29, 2017 / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS
RadiationMonochromator: CHANNEL CUT CRYOGENICALLY COOLED MONOCROMATOR CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.58→49.6 Å / Num. obs: 22805 / % possible obs: 99.3 % / Redundancy: 25.36 % / Biso Wilson estimate: 116.03 Å2 / Rsym value: 0.2 / Net I/σ(I): 13.16
Reflection shellResolution: 3.58→3.71 Å / Redundancy: 24.82 % / Mean I/σ(I) obs: 1.37 / Num. unique obs: 2070 / Rsym value: 0.2421 / % possible all: 93.54

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Processing

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

5akp


Resolution: 3.58→49.6 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.544
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1141 5 %RANDOM
Rwork0.198 ---
obs0.2 22805 99.1 %-
Displacement parametersBiso mean: 156.24 Å2
Baniso -1Baniso -2Baniso -3
1--3.354 Å20 Å20 Å2
2---3.354 Å20 Å2
3---6.708 Å2
Refinement stepCycle: 1 / Resolution: 3.58→49.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9374 0 86 2 9462
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019680HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1613208HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4443SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes228HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1491HARMONIC5
X-RAY DIFFRACTIONt_it9680HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.67
X-RAY DIFFRACTIONt_other_torsion4.06
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_contact11375SEMIHARMONIC4
LS refinement shellResolution: 3.58→3.75 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2911 138 5.02 %
Rwork0.2314 2611 -
all0.2345 2749 -
obs--92.79 %
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)
10.44030.3264-0.00890.64270.75481.7930.09-0.07760.03540.0144-0.09860.18740.1745-0.44110.0087-0.1371-0.1520.0141-0.29790.02380.1529-30.487837.7503-6.3356
20.63550.16040.76480.69890.642.55490.1169-0.0866-0.14990.14980.074-0.16250.30340.3678-0.1909-0.1653-0.1106-0.0543-0.27140.11140.1161-7.177737.6237-8.7551
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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