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- PDB-6bap: Stigmatella aurantiaca bacterial phytochrome PAS-GAF-PHY, T289H mutant -

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Basic information

Entry
Database: PDB / ID: 6bap
TitleStigmatella aurantiaca bacterial phytochrome PAS-GAF-PHY, T289H mutant
ComponentsPhotoreceptor-histidine kinase BphP
KeywordsSIGNALING PROTEIN / phytochrome / photosensory core module / T289H mutant
Function / homology
Function and homology information


detection of visible light / histidine kinase / phosphorelay sensor kinase activity / photoreceptor 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 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsSchmidt, M. / Stojkovic, E.
Funding support United States, 4items
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
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
C: Photoreceptor-histidine kinase BphP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,3996
Polymers172,6453
Non-polymers1,7543
Water2,234124
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
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-13 kcal/mol
Surface area44640 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
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area4700 Å2
ΔGint-16 kcal/mol
Surface area48470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.310, 83.310, 475.050
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
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.: 3
Source method: isolated from a genetically manipulated source
Formula: C33H36N4O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.82 Å3/Da / Density % sol: 56.33 %
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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 23, 2013
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: 2.65→42.6 Å / Num. obs: 56756 / % possible obs: 99.1 % / Redundancy: 3.5 % / CC1/2: 0.997 / Rpim(I) all: 0.041 / Rrim(I) all: 0.084 / Rsym value: 0.073 / Net I/σ(I): 7.9
Reflection shellResolution: 2.65→2.72 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4109 / CC1/2: 0.364 / Rpim(I) all: 0.553 / Rrim(I) all: 1.081 / Rsym value: 0.919 / % possible all: 99.1

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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 6BAO

6bao


Resolution: 2.65→40.284 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.78
RfactorNum. reflection% reflectionSelection details
Rfree0.3148 2870 5.07 %random
Rwork0.2411 ---
obs0.2448 56656 98.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.65→40.284 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11905 0 129 124 12158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01312325
X-RAY DIFFRACTIONf_angle_d1.57216732
X-RAY DIFFRACTIONf_dihedral_angle_d21.6477351
X-RAY DIFFRACTIONf_chiral_restr0.0751796
X-RAY DIFFRACTIONf_plane_restr0.0092206
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.69570.43071200.34562660X-RAY DIFFRACTION98
2.6957-2.74470.41111290.33952636X-RAY DIFFRACTION99
2.7447-2.79750.37491530.32962669X-RAY DIFFRACTION99
2.7975-2.85460.42171650.33012609X-RAY DIFFRACTION99
2.8546-2.91670.41841340.33322646X-RAY DIFFRACTION99
2.9167-2.98450.39981660.31342663X-RAY DIFFRACTION99
2.9845-3.05910.41421360.30272642X-RAY DIFFRACTION99
3.0591-3.14180.39121300.28642671X-RAY DIFFRACTION99
3.1418-3.23420.34611590.2712641X-RAY DIFFRACTION99
3.2342-3.33850.33961400.2722710X-RAY DIFFRACTION99
3.3385-3.45780.31931510.26042628X-RAY DIFFRACTION99
3.4578-3.59610.30981410.242664X-RAY DIFFRACTION98
3.5961-3.75970.30561570.23562635X-RAY DIFFRACTION99
3.7597-3.95780.31371320.22942705X-RAY DIFFRACTION99
3.9578-4.20550.27921210.2112684X-RAY DIFFRACTION99
4.2055-4.52980.28751430.20352715X-RAY DIFFRACTION99
4.5298-4.98490.2611110.20252771X-RAY DIFFRACTION99
4.9849-5.70450.31151520.2342741X-RAY DIFFRACTION99
5.7045-7.18040.34231700.25582803X-RAY DIFFRACTION99
7.1804-40.28910.26131600.21122893X-RAY DIFFRACTION96

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