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- PDB-6umz: Crystal structure of photoactive yellow protein (PYP); 3-Br-p-cou... -

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Basic information

Entry
Database: PDB / ID: 6umz
TitleCrystal structure of photoactive yellow protein (PYP); 3-Br-p-coumaric acid chromophore
ComponentsPhotoactive yellow protein
KeywordsSIGNALING PROTEIN / photoactive yellow protein
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
(2E)-3-(3-bromo-4-hydroxyphenyl)prop-2-enoic acid / Photoactive yellow protein
Similarity search - Component
Biological speciesHalorhodospira halophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.9 Å
AuthorsLin, C.-Y. / Romei, M.G. / Boxer, S.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)118044 United States
CitationJournal: J Photochem Photobiol A Chem / Year: 2020
Title: Structural and spectroscopic characterization of photoactive yellow protein and photoswitchable fluorescent protein constructs containing heavy atoms.
Authors: Romei, M.G. / Lin, C.Y. / Boxer, S.G.
History
DepositionOct 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2020Group: 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_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 4, 2020Group: Database references / Category: citation / Item: _citation.page_first
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)14,4142
Polymers14,1711
Non-polymers2431
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.767, 65.767, 40.577
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Photoactive yellow protein / PYP


Mass: 14170.851 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 BL21(DE3) (bacteria) / References: UniProt: P16113
#2: Chemical ChemComp-QBV / (2E)-3-(3-bromo-4-hydroxyphenyl)prop-2-enoic acid


Mass: 243.054 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7BrO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.79 Å3/Da / Density % sol: 31.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20 mM potassium phosphate, pH 6.0, 1 M NaCl, 1.9 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.88557 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88557 Å / Relative weight: 1
ReflectionResolution: 0.9→33.05 Å / Num. obs: 69351 / % possible obs: 93.7 % / Redundancy: 60.1 % / Biso Wilson estimate: 8.11 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.008 / Rrim(I) all: 0.065 / Net I/σ(I): 39.1 / Num. measured all: 4167073 / Scaling rejects: 285
Reflection shellResolution: 0.9→0.92 Å / Redundancy: 24.2 % / Rmerge(I) obs: 2.011 / Num. measured all: 68511 / Num. unique obs: 2834 / CC1/2: 0.656 / Rpim(I) all: 0.415 / Rrim(I) all: 2.055 / Net I/σ(I) obs: 1.9 / % possible all: 77.5

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Processing

Software
NameVersionClassification
PHENIX1.13RC2_2986refinement
Aimless0.7.3data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NWZ

1nwz


Resolution: 0.9→33.05 Å / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 12.79
RfactorNum. reflection% reflection
Rfree0.137 1997 2.88 %
Rwork0.127 67340 -
obs0.127 69337 93.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 52.38 Å2 / Biso mean: 13.02 Å2 / Biso min: 3.39 Å2
Refinement stepCycle: final / Resolution: 0.9→33.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms992 0 17 150 1159
Biso mean--7.8 20.67 -
Num. residues----127
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
0.9-0.92250.2461180.21833970408878
0.9225-0.94750.18861250.17864206433183
0.9475-0.97530.20951280.16274411453986
0.9753-1.00680.15451370.13274631476890
1.0068-1.04280.11771460.11364835498195
1.0428-1.08460.11011440.10524874501896
1.0846-1.13390.11781440.09914933507796
1.1339-1.19370.10011460.09484951509797
1.1937-1.26850.10181510.10064973512497
1.2685-1.36640.13891480.1045011515998
1.3664-1.5040.12921520.10985061521398
1.504-1.72160.12911520.11825089524199
1.7216-2.16890.14231510.12785137528899
2.1689-33.0480.1461550.146152585413100

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