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- PDB-6bay: Stigmatella aurantiaca bacterial phytochrome P1, PAS-GAF-PHY T289... -

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Basic information

Entry
Database: PDB / ID: 6bay
TitleStigmatella aurantiaca bacterial phytochrome P1, PAS-GAF-PHY T289H mutant, room temperature structure
ComponentsPhotoreceptor-histidine kinase BphP
KeywordsSIGNALING PROTEIN / bacterial phytochrome / Stigmatella aurantiaca / photosensory core module / PAS-GAF-PHY / room temperature / SACLA / T28H mutant
Function / homology
Function and homology information


osmosensory signaling via phosphorelay pathway / detection of visible light / phosphorelay response regulator activity / histidine kinase / phosphorelay sensor kinase activity / protein kinase activator activity / 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 / GAF domain / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. ...: / Phytochrome / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / GAF domain / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / PAS domain / 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 / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsSchmidt, M. / Stojkovic, E.
Funding support United States, Finland, 7items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)STC-1231306 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
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM095583 United States
Academy of Finland296135 Finland
Academy of Finland285461 Finland
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 16, 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
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
C: Photoreceptor-histidine kinase BphP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,3996
Polymers172,6453
Non-polymers1,7543
Water00
1
A: Photoreceptor-histidine kinase BphP
B: Photoreceptor-histidine kinase BphP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,2664
Polymers115,0962
Non-polymers1,1692
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-10 kcal/mol
Surface area45100 Å2
MethodPISA
2
C: Photoreceptor-histidine kinase BphP
hetero molecules

C: Photoreceptor-histidine kinase BphP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,2664
Polymers115,0962
Non-polymers1,1692
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area4910 Å2
ΔGint-14 kcal/mol
Surface area48100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.230, 84.230, 477.990
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 57548.180 Da / Num. of mol.: 3 / Fragment: PAS-GAF-PHY (UNP residues 1-515) / Mutation: T289H
Source method: isolated from a genetically manipulated source
Details: Stigmatella aurantiaca bacterial phytochrome P1, SaBphP1-PCM-T289H mutant
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


Mass: 584.662 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C33H36N4O6
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: 2.84 Å3/Da / Density % sol: 56.62 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.2
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: 293 K / Ambient temp details: room temperature in air, SACLA
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.3 Å
DetectorType: MPCCD / Detector: CCD / Date: Dec 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 3.15→53.8 Å / Num. obs: 52483 / % possible obs: 100 % / Redundancy: 399 % / CC1/2: 0.998 / Rmerge(I) obs: 0.0105 / Net I/σ(I): 4.76
Reflection shellResolution: 3.15→3.2 Å / Redundancy: 107 % / Num. unique obs: 1956 / CC1/2: 0.506 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6BAP

6bap


Resolution: 3.15→53.799 Å / SU ML: 0.65 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.03
RfactorNum. reflection% reflection
Rfree0.2819 1807 5 %
Rwork0.2215 --
obs0.2248 40760 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.15→53.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11905 0 129 0 12034
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01212325
X-RAY DIFFRACTIONf_angle_d1.59416732
X-RAY DIFFRACTIONf_dihedral_angle_d21.4777351
X-RAY DIFFRACTIONf_chiral_restr0.071796
X-RAY DIFFRACTIONf_plane_restr0.0092206
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0001-3.06990.4261210.38762435X-RAY DIFFRACTION97
3.0699-3.14660.40681250.36472549X-RAY DIFFRACTION100
3.1466-3.23170.36691300.33752564X-RAY DIFFRACTION100
3.2317-3.32680.381100.31832561X-RAY DIFFRACTION100
3.3268-3.43420.33431440.29862498X-RAY DIFFRACTION100
3.4342-3.55690.35561380.27932569X-RAY DIFFRACTION100
3.5569-3.69920.3491510.25882543X-RAY DIFFRACTION100
3.6992-3.86760.32811400.24022557X-RAY DIFFRACTION100
3.8676-4.07140.31231240.21882586X-RAY DIFFRACTION100
4.0714-4.32640.28681120.19532598X-RAY DIFFRACTION100
4.3264-4.66030.23531460.1862605X-RAY DIFFRACTION100
4.6603-5.12890.26551310.20362578X-RAY DIFFRACTION100
5.1289-5.87030.3191560.2292630X-RAY DIFFRACTION100
5.8703-7.39290.29461450.24532684X-RAY DIFFRACTION100
7.3929-53.80780.24041640.192766X-RAY DIFFRACTION97

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