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- PDB-6mmd: Photoactive Yellow Protein with 3,5-dichlorotyrosine substituted ... -

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Basic information

Entry
Database: PDB / ID: 6mmd
TitlePhotoactive Yellow Protein with 3,5-dichlorotyrosine 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: 1.228 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 30, 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

Downloads & links

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Assembly

Deposited unit
A: Photoactive yellow protein
B: Photoactive yellow protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2434
Polymers27,9152
Non-polymers3282
Water4,918273
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.909, 65.909, 40.503
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-430-

HOH

21A-431-

HOH

31B-441-

HOH

41B-442-

HOH

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Components

#1: Protein Photoactive yellow protein / PYP


Mass: 13957.466 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: C9H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 1.82 Å3/Da / Density % sol: 32.47 %
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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.228→50 Å / Num. obs: 56619 / % possible obs: 98.5 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 49.03
Reflection shellResolution: 1.228→1.27 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
DENZOdata reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NWZ

1nwz


Resolution: 1.228→33.032 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 17.91
RfactorNum. reflection% reflection
Rfree0.181 2924 5.16 %
Rwork0.1532 --
obs0.1547 56617 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.228→33.032 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1956 0 22 273 2251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152022
X-RAY DIFFRACTIONf_angle_d1.4462720
X-RAY DIFFRACTIONf_dihedral_angle_d14.816726
X-RAY DIFFRACTIONf_chiral_restr0.092280
X-RAY DIFFRACTIONf_plane_restr0.01360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2285-1.24860.27691600.25512256X-RAY DIFFRACTION90
1.2486-1.27020.26621190.22982522X-RAY DIFFRACTION97
1.2702-1.29330.22961370.21852508X-RAY DIFFRACTION98
1.2933-1.31810.2261560.20372529X-RAY DIFFRACTION98
1.3181-1.3450.20321080.18832645X-RAY DIFFRACTION99
1.345-1.37430.21421580.1872528X-RAY DIFFRACTION99
1.3743-1.40630.20571290.18912610X-RAY DIFFRACTION100
1.4063-1.44140.25851050.18472603X-RAY DIFFRACTION100
1.4414-1.48040.17421400.18332542X-RAY DIFFRACTION99
1.4804-1.5240.1981500.1742547X-RAY DIFFRACTION99
1.524-1.57310.20761700.16542594X-RAY DIFFRACTION100
1.5731-1.62940.21381000.15742620X-RAY DIFFRACTION100
1.6294-1.69460.16521460.15912551X-RAY DIFFRACTION100
1.6946-1.77170.19151650.1592592X-RAY DIFFRACTION100
1.7717-1.86510.19481280.15552594X-RAY DIFFRACTION99
1.8651-1.9820.18871500.15082557X-RAY DIFFRACTION100
1.982-2.1350.16821150.14142635X-RAY DIFFRACTION100
2.135-2.34980.16971350.14432573X-RAY DIFFRACTION99
2.3498-2.68970.18821600.15032534X-RAY DIFFRACTION99
2.6897-3.38810.1891850.15012541X-RAY DIFFRACTION100
3.3881-33.04370.13111080.13022612X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.84380.16020.06711.9168-0.41551.9752-0.03080.02820.09520.0075-0.0285-0.133-0.17680.1370.03950.1175-0.0137-0.00810.11810.00280.123844.745936.4654-0.5276
21.4244-0.56620.35491.2626-0.21921.8954-0.03990.00030.1506-0.0137-0.01020.0161-0.2043-0.08570.03590.13010.0076-0.00660.1084-0.00520.123323.746937.9577-20.7811
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 125)
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 125)

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