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- PDB-6bao: Stigmatella aurantiaca phytochrome photosensory core module, wild type -

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Basic information

Entry
Database: PDB / ID: 6bao
TitleStigmatella aurantiaca phytochrome photosensory core module, wild type
ComponentsPhotoreceptor-histidine kinase BphP
KeywordsSIGNALING PROTEIN / phytochrome / PAS-GAF-PHY
Function / homology
Function and homology information


detection of visible light / histidine kinase / photoreceptor activity / phosphorelay sensor kinase activity / regulation of DNA-templated transcription
Similarity search - Function
PHY 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. / GAF domain ...PHY 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. / GAF domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / PAS 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 / Beta-Lactamase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-BLR / histidine kinase
Similarity search - Component
Biological speciesStigmatella aurantiaca DW4/3-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsSchmidt, M. / Stojkovic, E.
Funding support United States, 4items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)STC1231306 United States
National Science Foundation (NSF, United States)BIO-MCB 1413360 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T34 GM105549-01 NU-STARS United States
National Institutes of Health/National Eye Institute (NIH/NEI)EY024363 United States
CitationJournal: IUCrJ / Year: 2018
Title: Structural basis for light control of cell development revealed by crystal structures of a myxobacterial phytochrome.
Authors: Woitowich, N.C. / Halavaty, A.S. / Waltz, P. / Kupitz, C. / Valera, J. / Tracy, G. / Gallagher, K.D. / Claesson, E. / Nakane, T. / Pandey, S. / Nelson, G. / Tanaka, R. / Nango, E. / ...Authors: Woitowich, N.C. / Halavaty, A.S. / Waltz, P. / Kupitz, C. / Valera, J. / Tracy, G. / Gallagher, K.D. / Claesson, E. / Nakane, T. / Pandey, S. / Nelson, G. / Tanaka, R. / Nango, E. / Mizohata, E. / Owada, S. / Tono, K. / Joti, Y. / Nugent, A.C. / Patel, H. / Mapara, A. / Hopkins, J. / Duong, P. / Bizhga, D. / Kovaleva, S.E. / St Peter, R. / Hernandez, C.N. / Ozarowski, W.B. / Roy-Chowdhuri, S. / Yang, J.H. / Edlund, P. / Takala, H. / Ihalainen, J. / Brayshaw, J. / Norwood, T. / Poudyal, I. / Fromme, P. / Spence, J.C.H. / Moffat, K. / Westenhoff, S. / Schmidt, M. / Stojkovic, E.A.
History
DepositionOct 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)115,7074
Polymers114,5382
Non-polymers1,1692
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-11 kcal/mol
Surface area44660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.510, 134.990, 113.180
Angle α, β, γ (deg.)90.00, 105.90, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-775-

HOH

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Components

#1: Protein Photoreceptor-histidine kinase BphP / Sensor protein


Mass: 57268.859 Da / Num. of mol.: 2 / Fragment: PAS-GAF-PHY (UNP residues 1-513)
Source method: isolated from a genetically manipulated source
Details: phytochrome photosensory core domain, dimer
Source: (gene. exp.) Stigmatella aurantiaca DW4/3-1 (bacteria)
Strain: DW4/3-1 / Gene: STAUR_8015, STIAU_3396 / Production host: Escherichia coli (E. coli) / References: UniProt: Q097N3
#2: Chemical ChemComp-BLR / 3-[5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-2-[[5-[(Z)-(3-ethenyl-4-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1H-pyrrol-2-yl]methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid / Bilirubin IX alpha / Bilirubin


Mass: 584.662 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C33H36N4O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.65 Å3/Da / Density % sol: 53.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 11 mg/mL protein in 0.1 M MES, pH 6.2, 8-5% w/v PEG20000, 5.2% v/v acetonitrile

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 15, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.18→39 Å / Num. obs: 69342 / % possible obs: 98 % / Redundancy: 4.8 % / Net I/σ(I): 6.7
Reflection shellResolution: 2.18→2.24 Å / Redundancy: 3.1 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 3403 / CC1/2: 0.387 / Rpim(I) all: 0.687 / % possible all: 75

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4Q0J

4q0j


Resolution: 2.18→38.4 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.21
RfactorNum. reflection% reflection
Rfree0.2622 2903 4.91 %
Rwork0.2195 --
obs0.2217 68058 78.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.18→38.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7924 0 86 271 8281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118202
X-RAY DIFFRACTIONf_angle_d1.3511136
X-RAY DIFFRACTIONf_dihedral_angle_d21.4474894
X-RAY DIFFRACTIONf_chiral_restr0.061198
X-RAY DIFFRACTIONf_plane_restr0.0071468
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9505-1.97840.4171140.5099238X-RAY DIFFRACTION7
1.9784-2.00790.3471200.4562509X-RAY DIFFRACTION15
2.0079-2.03930.4706470.4097881X-RAY DIFFRACTION26
2.0393-2.07270.3689750.40731250X-RAY DIFFRACTION36
2.0727-2.10840.3835660.38921593X-RAY DIFFRACTION46
2.1084-2.14680.4294950.38011892X-RAY DIFFRACTION56
2.1468-2.1880.40311250.37222098X-RAY DIFFRACTION62
2.188-2.23270.43411440.34632537X-RAY DIFFRACTION74
2.2327-2.28120.35731430.33033036X-RAY DIFFRACTION89
2.2812-2.33430.36521730.31163347X-RAY DIFFRACTION97
2.3343-2.39270.33091630.28353324X-RAY DIFFRACTION98
2.3927-2.45740.3581760.27733352X-RAY DIFFRACTION98
2.4574-2.52970.34841700.26443347X-RAY DIFFRACTION98
2.5297-2.61130.2881780.26053391X-RAY DIFFRACTION99
2.6113-2.70460.28241990.26443343X-RAY DIFFRACTION98
2.7046-2.81280.28981650.26133402X-RAY DIFFRACTION99
2.8128-2.94080.31281650.25243407X-RAY DIFFRACTION99
2.9408-3.09580.28441790.24993363X-RAY DIFFRACTION99
3.0958-3.28970.28941590.24583448X-RAY DIFFRACTION99
3.2897-3.54350.29181730.21513367X-RAY DIFFRACTION99
3.5435-3.89980.23871900.19933410X-RAY DIFFRACTION99
3.8998-4.46340.22091490.17333436X-RAY DIFFRACTION99
4.4634-5.62050.21742060.1743422X-RAY DIFFRACTION99
5.6205-38.40780.211670.18213324X-RAY DIFFRACTION95

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