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- PDB-6bak: The structure of the Stigmatella aurantiaca phytochrome chromopho... -

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Basic information

Entry
Database: PDB / ID: 6bak
TitleThe structure of the Stigmatella aurantiaca phytochrome chromophore binding domain T289H mutant
ComponentsPhotoreceptor-histidine kinase BphP
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


osmosensory signaling via phosphorelay pathway / detection of visible light / phosphorelay response regulator activity / phosphorelay sensor kinase activity / histidine kinase / photoreceptor activity / protein kinase activator activity / regulation of DNA-templated transcription
Similarity search - Function
Phytochrome / : / Phytochrome, PHY domain superfamily / Phytochrome, central region / PAS fold-2 / PAS fold / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / His Kinase A (phospho-acceptor) domain ...Phytochrome / : / Phytochrome, PHY domain superfamily / Phytochrome, central region / PAS fold-2 / PAS fold / Phytochrome region / 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 / 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 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: 1.92 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 13, 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 1.5Nov 20, 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: Photoreceptor-histidine kinase BphP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4052
Polymers33,8211
Non-polymers5851
Water5,783321
1
A: Photoreceptor-histidine kinase BphP
hetero molecules

A: Photoreceptor-histidine kinase BphP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8114
Polymers67,6412
Non-polymers1,1692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area2570 Å2
ΔGint-13 kcal/mol
Surface area25810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.449, 131.449, 95.741
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-605-

HOH

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Components

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


Mass: 33820.625 Da / Num. of mol.: 1
Fragment: Phytochrome chromophore binding domain (UNP residues 16-318)
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


Mass: 584.662 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H36N4O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 7.06 Å3/Da / Density % sol: 82.58 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.07 M sodium acetate trihydrate, pH 4.6, 1.4 M sodium formate, 30% w/v glycerol

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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: Oct 27, 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: 2.03→100 Å / Num. obs: 71587 / % possible obs: 98 % / Redundancy: 4.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.049 / Net I/σ(I): 6.4
Reflection shellResolution: 2.03→2.08 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.989 / Num. unique obs: 4196 / CC1/2: 0.416 / Rpim(I) all: 0.746 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4RQ9

4rq9


Resolution: 1.92→23.423 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2248 3638 5.1 %RANDOM
Rwork0.2056 ---
obs0.2065 71392 97.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.92→23.423 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2383 0 43 321 2747
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182488
X-RAY DIFFRACTIONf_angle_d1.8223386
X-RAY DIFFRACTIONf_dihedral_angle_d18.0151484
X-RAY DIFFRACTIONf_chiral_restr0.123367
X-RAY DIFFRACTIONf_plane_restr0.009444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9201-1.94540.41921230.38972450X-RAY DIFFRACTION92
1.9454-1.9720.3351330.35172588X-RAY DIFFRACTION98
1.972-2.00020.3381610.35032568X-RAY DIFFRACTION98
2.0002-2.030.34011280.32932600X-RAY DIFFRACTION98
2.03-2.06170.33781480.32652611X-RAY DIFFRACTION99
2.0617-2.09550.33031450.30932585X-RAY DIFFRACTION98
2.0955-2.13160.31271430.28452582X-RAY DIFFRACTION98
2.1316-2.17030.26471470.26532612X-RAY DIFFRACTION99
2.1703-2.21210.27461380.27872587X-RAY DIFFRACTION99
2.2121-2.25720.27761310.2762647X-RAY DIFFRACTION99
2.2572-2.30620.2961550.27282588X-RAY DIFFRACTION99
2.3062-2.35980.28641170.26872628X-RAY DIFFRACTION99
2.3598-2.41880.30851640.26972604X-RAY DIFFRACTION99
2.4188-2.48410.28541450.26372600X-RAY DIFFRACTION99
2.4841-2.55710.27261640.24692617X-RAY DIFFRACTION99
2.5571-2.63950.29521180.23272669X-RAY DIFFRACTION99
2.6395-2.73370.25121420.23842632X-RAY DIFFRACTION99
2.7337-2.8430.24981310.22632644X-RAY DIFFRACTION99
2.843-2.97220.25131510.21982641X-RAY DIFFRACTION99
2.9722-3.12850.23261420.21242660X-RAY DIFFRACTION99
3.1285-3.3240.20371490.19932634X-RAY DIFFRACTION99
3.324-3.57980.2121230.18332671X-RAY DIFFRACTION99
3.5798-3.93860.17831530.15892669X-RAY DIFFRACTION100
3.9386-4.5050.15691410.14482693X-RAY DIFFRACTION99
4.505-5.66250.181240.15422717X-RAY DIFFRACTION99
5.6625-23.42480.19811220.1972257X-RAY DIFFRACTION80

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