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- PDB-6un2: Crystal structure of photoactive yellow protein (PYP); C69U const... -

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Basic information

Entry
Database: PDB / ID: 6un2
TitleCrystal structure of photoactive yellow protein (PYP); C69U construct (selenocysteine incorporation)
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 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: 0.97 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

Downloads & links

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Assembly

Deposited unit
A: Photoactive yellow protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3822
Polymers14,2181
Non-polymers1641
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.859, 65.859, 40.531
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: 14217.747 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.: 109 / 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: 31.08 %
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: BL12-2 / Wavelength: 0.72929 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.72929 Å / Relative weight: 1
ReflectionResolution: 0.97→23.323 Å / Num. obs: 59305 / % possible obs: 99.9 % / Redundancy: 40.229 % / Biso Wilson estimate: 9.96 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.083 / Χ2: 1.025 / Net I/σ(I): 23.8 / Num. measured all: 2385798 / Scaling rejects: 174
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
0.97-138.6542.7291.15166366438643040.5532.76498.1
1-1.0240.9371.9931.82174104425542530.7312.018100
1.02-1.0540.471.5972.4166533411541150.8241.617100
1.05-1.0939.8581.1233.55161385405040490.9081.137100
1.09-1.1238.0090.8045.1149298392939280.9490.815100
1.12-1.1639.3140.6516.57147625375537550.9670.659100
1.16-1.241.5170.5378.37151330364536450.9780.544100
1.2-1.2541.4740.4659.67145616351135110.9850.471100
1.25-1.3141.120.3812.05139233338633860.9890.385100
1.31-1.3739.7030.30914.5127406320932090.9930.313100
1.37-1.4538.4480.23618.68117883306630660.9950.239100
1.45-1.5442.8720.17826.06124501290529040.9980.18100
1.54-1.6442.4870.14133.05115863272727270.9990.142100
1.64-1.7741.7070.10543.64106520255425540.9990.106100
1.77-1.9438.7870.07855.5791304235423540.9990.079100
1.94-2.1739.3020.05573.6830452113211310.056100
2.17-2.5141.9880.04888.03788541878187810.048100
2.51-3.0740.2410.04100.29642251596159610.04100
3.07-4.3436.8270.032114.6461441253125310.032100
4.34-23.32340.5150.032125.382856370670510.03399.9

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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: 0.97→23.323 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 14.25
RfactorNum. reflection% reflection
Rfree0.1567 2959 4.99 %
Rwork0.1338 --
obs0.1349 59303 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 52.96 Å2 / Biso mean: 14.0969 Å2 / Biso min: 6.3 Å2
Refinement stepCycle: final / Resolution: 0.97→23.323 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms971 0 17 109 1097
Biso mean--8.32 22.69 -
Num. residues----125
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
0.97-0.98540.27821360.2646262798
0.9854-1.00240.24311430.22332656100
1.0024-1.02070.22251400.21322653100
1.0207-1.04030.23111400.20092674100
1.0403-1.06150.18951390.17432700100
1.0615-1.08460.17881390.15682663100
1.0846-1.10980.15481400.14372671100
1.1098-1.13760.15541400.13042696100
1.1376-1.16830.14031410.11982657100
1.1683-1.20270.12471420.1172666100
1.2027-1.24150.13811440.11562690100
1.2415-1.28590.11841390.11122675100
1.2859-1.33740.13631440.11152683100
1.3374-1.39820.12661430.10772682100
1.3982-1.4720.11761390.10432672100
1.472-1.56420.12561430.10412695100
1.5642-1.68490.13841370.10472718100
1.6849-1.85440.141410.10932666100
1.8544-2.12260.12541410.11992719100
2.1226-2.67360.15981400.13882716100
2.6736-23.3230.18971480.15442765100

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