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- PDB-6mhi: Photoactive Yellow Protein with covalently bound 3,5-dichloro-4-h... -

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Basic information

Entry
Database: PDB / ID: 6mhi
TitlePhotoactive Yellow Protein with covalently bound 3,5-dichloro-4-hydroxycinnamic acid chromophore
ComponentsPhotoactive yellow protein
KeywordsSIGNALING PROTEIN / chlorinated chromophore / hydrogen bonding network / active site / low-barrier hydrogen bond
Function / homology
Function and homology information


photoreceptor activity / phototransduction / regulation of DNA-templated transcription / identical protein binding
Similarity search - Function
Photoactive yellow-protein / PAS domain / Beta-Lactamase / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-YYZ / Photoactive yellow protein
Similarity search - Component
Biological speciesHalorhodospira halophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsThomson, B.D. / Both, J. / Wu, Y. / Parrish, R.M. / Martinez, T. / Boxer, S.G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorR35GM11804401 United States
National Science Foundation (NSF, United States)CHE-17406456 United States
CitationJournal: J.Phys.Chem.B / Year: 2019
Title: Perturbation of Short Hydrogen Bonds in Photoactive Yellow Protein via Noncanonical Amino Acid Incorporation.
Authors: Thomson, B. / Both, J. / Wu, Y. / Parrish, R.M. / Martinez, T.J. / Boxer, S.G.
History
DepositionSep 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 26, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 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: Photoactive yellow protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1222
Polymers13,8891
Non-polymers2331
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.970, 65.970, 40.420
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

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Components

#1: Protein Photoactive yellow protein / PYP


Mass: 13888.575 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halorhodospira halophila (bacteria) / Gene: pyp / Production host: Escherichia coli (E. coli) / References: UniProt: P16113
#2: Chemical ChemComp-YYZ / (2E)-3-(3,5-dichloro-4-hydroxyphenyl)prop-2-enoic acid


Mass: 233.048 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H6Cl2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 1.83 Å3/Da / Density % sol: 32.72 % / Description: Hexagonal prismatic
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1M sodium chloride, 2.4M ammonium sulfate, pH = 6.0, drops were microseeded

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.88558 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88558 Å / Relative weight: 1
ReflectionResolution: 1.28→40.46 Å / Num. obs: 24905 / % possible obs: 62.8 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.013 / Net I/σ(I): 25.1
Reflection shellHighest resolution: 1.28 Å

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Processing

Software
NameClassification
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NWZ

1nwz


Resolution: 1.35→40.46 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.1863 -5 %
Rwork0.1435 --
obs-24893 100 %
Refinement stepCycle: LAST / Resolution: 1.35→40.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms976 0 13 98 1087

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