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- PDB-6mkt: Photoactive Yellow Protein with 3-chlorotyrosine substituted at p... -

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Basic information

Entry
Database: PDB / ID: 6mkt
TitlePhotoactive Yellow Protein with 3-chlorotyrosine substituted at position 42
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
4'-HYDROXYCINNAMIC ACID / Photoactive yellow protein
Similarity search - Component
Biological speciesHalorhodospira halophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 26, 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)14,0872
Polymers13,9231
Non-polymers1641
Water1,65792
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)65.500, 65.500, 40.380
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: 13923.021 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-HC4 / 4'-HYDROXYCINNAMIC ACID / PARA-COUMARIC ACID


Mass: 164.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 1.75 Å3/Da / Density % sol: 29.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
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: SSRL / Beamline: BL14-1 / Wavelength: 1.18076 Å
DetectorType: RAYONIX MX325HE / Detector: CCD / Date: Nov 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18076 Å / Relative weight: 1
ReflectionResolution: 1.21→50 Å / Num. obs: 13140 / % possible obs: 77.5 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 14
Reflection shellResolution: 1.21→1.23 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
MOSFLMdata reduction
PROTEUM PLUSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NWZ

1nwz


Resolution: 1.6→32.896 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.93
RfactorNum. reflection% reflection
Rfree0.1888 636 4.84 %
Rwork0.1665 --
obs0.1675 13140 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→32.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms977 0 11 92 1080
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061019
X-RAY DIFFRACTIONf_angle_d0.881371
X-RAY DIFFRACTIONf_dihedral_angle_d14.654595
X-RAY DIFFRACTIONf_chiral_restr0.059142
X-RAY DIFFRACTIONf_plane_restr0.004182
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.72350.22531360.17822451X-RAY DIFFRACTION100
1.7235-1.8970.21091270.17372477X-RAY DIFFRACTION100
1.897-2.17140.21011270.16482509X-RAY DIFFRACTION100
2.1714-2.73550.18721430.17452498X-RAY DIFFRACTION100
2.7355-32.90320.16891030.15952569X-RAY DIFFRACTION100

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