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- PDB-6umy: Crystal structure of photoactive yellow protein (PYP); F96(4-IF) ... -

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Basic information

Entry
Database: PDB / ID: 6umy
TitleCrystal structure of photoactive yellow protein (PYP); F96(4-IF) construct
ComponentsPhotoactive yellow protein
KeywordsSIGNALING 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 fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily
Similarity search - Domain/homology
4'-HYDROXYCINNAMIC ACID / Photoactive yellow protein
Similarity search - Component
Biological speciesHalorhodospira halophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.923 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

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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)14,4612
Polymers14,2971
Non-polymers1641
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.852, 65.852, 40.591
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: 14296.749 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) / Strain (production host): BL21(DE3) / 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.78 Å3/Da / Density % sol: 30.79 %
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: 0.92→33.07 Å / Num. obs: 67974 / % possible obs: 98.6 % / Redundancy: 24.648 % / Biso Wilson estimate: 7.7 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.049 / Χ2: 1.087 / Net I/σ(I): 32.27 / Num. measured all: 1675455
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
0.92-0.9514.8281.6961.4566950508445150.61.75688.8
0.95-0.9715.8041.3651.9574562494247180.7341.40995.5
0.97-117.590.9982.8481985479446610.8551.02797.2
1-1.0319.4490.7773.9490457469946510.9190.79899
1.03-1.0620.0210.5655.590333451645120.9560.5899.9
1.06-1.122.0350.4068.1797242441544130.980.415100
1.1-1.1422.3360.3210.6493944420642060.9880.327100
1.14-1.1922.0140.24513.7590303410241020.9910.251100
1.19-1.2424.060.20617.1493785389838980.9950.21100
1.24-1.324.5230.17220.8491740374137410.9960.176100
1.3-1.3724.5450.14824.2287798357735770.9970.152100
1.37-1.4626.680.11432.990231338233820.9980.116100
1.46-1.5629.3420.08744.1192514315331530.9990.089100
1.56-1.6831.570.07156.0193984297729770.9990.073100
1.68-1.8435.8690.05476.1970972707270710.055100
1.84-2.0641.2080.041103.31012472457245710.042100
2.06-2.3839.8410.034121.94872122189218910.035100
2.38-2.9135.4850.03128.8656821851185110.03100
2.91-4.1240.560.024164.47585281443144310.025100
4.12-33.0736.3710.023162.042986182282110.02399.9

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.13rc2_2986refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NWZ

1nwz


Resolution: 0.923→33.07 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 12.57
RfactorNum. reflection% reflection
Rfree0.1383 2017 2.97 %
Rwork0.1226 --
obs0.123 67945 98.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 54.74 Å2 / Biso mean: 12.8196 Å2 / Biso min: 4.68 Å2
Refinement stepCycle: final / Resolution: 0.923→33.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms962 0 17 114 1093
Biso mean--7.01 20.76 -
Num. residues----124
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
0.923-0.94560.251280.2543419888
0.9456-0.97120.19831370.2143452795
0.9712-0.99980.15751430.1753462997
0.9998-1.0320.14961430.1491470499
1.032-1.06890.13631450.12884743100
1.0689-1.11170.10851470.10864774100
1.1117-1.16230.12111420.10164765100
1.1623-1.22360.12251430.09984771100
1.2236-1.30030.11791460.09724761100
1.3003-1.40070.11081470.09744793100
1.4007-1.54160.12651460.09784776100
1.5416-1.76470.11371490.09794791100
1.7647-2.22330.13541450.11344812100
2.2233-33.070.15691560.14174884100

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