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- PDB-6baf: Structure of the chromophore binding domain of Stigmatella aurant... -

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Basic information

Entry
Database: PDB / ID: 6baf
TitleStructure of the chromophore binding domain of Stigmatella aurantiaca phytochrome P1, wild-type
ComponentsPhotoreceptor-histidine kinase BphP
KeywordsSIGNALING PROTEIN
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
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. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) 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. / 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 / Histidine kinase domain / Histidine kinase domain profile. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / 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
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: 1.85 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 12, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionSep 19, 2018ID: 4RPW
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

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Assembly

Deposited unit
A: Photoreceptor-histidine kinase BphP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3682
Polymers33,7841
Non-polymers5851
Water3,855214
1
A: Photoreceptor-histidine kinase BphP
hetero molecules

A: Photoreceptor-histidine kinase BphP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7364
Polymers67,5672
Non-polymers1,1692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area2650 Å2
ΔGint-12 kcal/mol
Surface area26010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.689, 131.689, 96.071
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-568-

HOH

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Components

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


Mass: 33783.582 Da / Num. of mol.: 1
Fragment: Phytochrome chromophore binding domain (UNP residues 16-318)
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.: 1 / Source method: obtained synthetically / Formula: C33H36N4O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 7.12 Å3/Da / Density % sol: 82.72 % / Description: hexagonal plates
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 65 mM Tris-HCl, pH 8.5, 5.2% w/v PEG8000, 35% v/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: 2.23→13.9 Å / Num. obs: 81078 / % possible obs: 99 % / Redundancy: 4.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.073 / Net I/σ(I): 6.3
Reflection shellResolution: 2.23→2.3 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.07 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 4168 / CC1/2: 0.36 / Rpim(I) all: 0.9 / % possible all: 99

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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 4RPW

4rpw
PDB Unreleased entry


Resolution: 1.85→23.502 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2283 3807 5.04 %RANDOM
Rwork0.2108 ---
obs0.2117 75590 92.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→23.502 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2380 0 43 214 2637
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162519
X-RAY DIFFRACTIONf_angle_d1.7433434
X-RAY DIFFRACTIONf_dihedral_angle_d17.9221512
X-RAY DIFFRACTIONf_chiral_restr0.103372
X-RAY DIFFRACTIONf_plane_restr0.009452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.87340.3993650.39911493X-RAY DIFFRACTION52
1.8734-1.8980.4426840.3811665X-RAY DIFFRACTION58
1.898-1.9240.3857910.37841621X-RAY DIFFRACTION57
1.924-1.95150.31621020.38291820X-RAY DIFFRACTION65
1.9515-1.98060.38711330.37022415X-RAY DIFFRACTION84
1.9806-2.01160.37271570.36882692X-RAY DIFFRACTION94
2.0116-2.04450.35991800.36452768X-RAY DIFFRACTION97
2.0445-2.07980.38531550.35512806X-RAY DIFFRACTION99
2.0798-2.11750.35531520.3372854X-RAY DIFFRACTION99
2.1175-2.15820.33511510.322807X-RAY DIFFRACTION99
2.1582-2.20230.36311350.31442844X-RAY DIFFRACTION99
2.2023-2.25010.34431420.3072844X-RAY DIFFRACTION99
2.2501-2.30240.33111410.3032846X-RAY DIFFRACTION99
2.3024-2.35990.31291660.28232848X-RAY DIFFRACTION99
2.3599-2.42370.28851680.27492830X-RAY DIFFRACTION99
2.4237-2.49490.27411410.26032851X-RAY DIFFRACTION99
2.4949-2.57540.25061350.2382892X-RAY DIFFRACTION99
2.5754-2.66730.23471680.21382833X-RAY DIFFRACTION99
2.6673-2.77390.21221350.21792884X-RAY DIFFRACTION100
2.7739-2.90.22231390.2192877X-RAY DIFFRACTION100
2.9-3.05250.22531330.21022893X-RAY DIFFRACTION99
3.0525-3.24330.2291500.19912893X-RAY DIFFRACTION100
3.2433-3.4930.21131670.19032870X-RAY DIFFRACTION100
3.493-3.84320.18691600.17092903X-RAY DIFFRACTION100
3.8432-4.39610.16141310.152963X-RAY DIFFRACTION100
4.3961-5.52670.16431410.1572939X-RAY DIFFRACTION100
5.5267-23.5040.21611850.1942832X-RAY DIFFRACTION94

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