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- PDB-6mhn: Photoactive Yellow Protein with covalently bound 3-chloro-4-hydro... -

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Basic information

Entry
Database: PDB / ID: 6mhn
TitlePhotoactive Yellow Protein with covalently bound 3-chloro-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-YAZ / Photoactive yellow protein
Similarity search - Component
Biological speciesHalorhodospira halophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 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
Revision 1.5Nov 20, 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: Photoactive yellow protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0872
Polymers13,8891
Non-polymers1991
Water1,63991
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)66.250, 66.250, 40.661
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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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-YAZ / (2E)-3-(3-chloro-4-hydroxyphenyl)prop-2-enoic acid


Mass: 198.603 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7ClO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 1.85 Å3/Da / Density % sol: 33.68 %
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: 1.00002 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 1.67→57.37 Å / Num. obs: 17696 / % possible obs: 99 % / Redundancy: 21.7 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 5.6
Reflection shellResolution: 1.67→1.71 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NWZ

1nwz


Resolution: 1.67→33.175 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.21
RfactorNum. reflection% reflection
Rfree0.2147 576 4.82 %
Rwork0.1701 --
obs0.1724 11942 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.67→33.175 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms972 0 0 91 1063
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061016
X-RAY DIFFRACTIONf_angle_d0.8691369
X-RAY DIFFRACTIONf_dihedral_angle_d2.556815
X-RAY DIFFRACTIONf_chiral_restr0.056141
X-RAY DIFFRACTIONf_plane_restr0.005183
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.83810.22431520.17332814X-RAY DIFFRACTION100
1.8381-2.1040.23091170.17042835X-RAY DIFFRACTION100
2.104-2.65070.24991490.18242843X-RAY DIFFRACTION100
2.6507-33.18110.19111580.16262874X-RAY DIFFRACTION100

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