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- PDB-9d10: Photoactive Yellow Protein, crystals from PEG, room temperature -

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Basic information

Entry
Database: PDB / ID: 9d10
TitlePhotoactive Yellow Protein, crystals from PEG, room temperature
ComponentsPhotoactive yellow protein
KeywordsSIGNALING PROTEIN / photoactive yellow protein / phototaxis
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: 1.8 Å
AuthorsMalla, T.N. / Schmidt, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1231306 United States
National Science Foundation (NSF, United States)2423601 United States
CitationJournal: Iucrj / Year: 2025
Title: Exploiting fourth-generation synchrotron radiation for enzyme and photoreceptor characterization.
Authors: Malla, T.N. / Muniyappan, S. / Menendez, D. / Ogukwe, F. / Dale, A.N. / Clayton, J.D. / Weatherall, D.D. / Karki, P. / Dangi, S. / Mandella, V. / Pacheco, A.A. / Stojkovic, E.A. / Rose, S.L. ...Authors: Malla, T.N. / Muniyappan, S. / Menendez, D. / Ogukwe, F. / Dale, A.N. / Clayton, J.D. / Weatherall, D.D. / Karki, P. / Dangi, S. / Mandella, V. / Pacheco, A.A. / Stojkovic, E.A. / Rose, S.L. / Orlans, J. / Basu, S. / de Sanctis, D. / Schmidt, M.
History
DepositionAug 7, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)14,0532
Polymers13,8891
Non-polymers1641
Water93752
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.360, 41.360, 118.870
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

#1: Protein Photoactive yellow protein / PYP


Mass: 13888.575 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.11 Å3/Da / Density % sol: 41.8 %
Crystal growTemperature: 292 K / Method: batch mode / pH: 6.5 / Details: 100 mM MES, 40% PEG 4000 / Temp details: room temperature

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Data collection

DiffractionMean temperature: 293 K / Ambient temp details: room temperature / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.1 Å
DetectorType: PSI JUNGFRAU 4M / Detector: PIXEL / Date: Feb 3, 2023
RadiationMonochromator: multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.8→118 Å / Num. obs: 2377266 / % possible obs: 100 % / Redundancy: 135 % / Biso Wilson estimate: 27.83 Å2 / CC1/2: 0.99 / R split: 0.1 / Net I/σ(I): 5
Reflection shellResolution: 1.8→1.85 Å / Num. unique obs: 513 / CC1/2: 0.65 / R split: 3
Serial crystallography measurementSource size: 4 µm2
Serial crystallography sample deliveryDescription: fixed target scan / Method: fixed target
Serial crystallography data reductionCrystal hits: 36668 / Lattices indexed: 37078

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→35.82 Å / SU ML: 0.2234 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 26.116
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.198 500 5.16 %
Rwork0.1525 9189 -
obs0.1548 9689 91.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.75 Å2
Refinement stepCycle: LAST / Resolution: 1.8→35.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms976 0 11 52 1039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00631035
X-RAY DIFFRACTIONf_angle_d0.81871395
X-RAY DIFFRACTIONf_chiral_restr0.0524147
X-RAY DIFFRACTIONf_plane_restr0.004185
X-RAY DIFFRACTIONf_dihedral_angle_d17.7657380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.980.3374850.3351867X-RAY DIFFRACTION73.69
1.98-2.270.30081470.19732290X-RAY DIFFRACTION92.63
2.27-2.860.20381420.19122473X-RAY DIFFRACTION98.38
2.86-35.820.15711260.10972559X-RAY DIFFRACTION99.67
Refinement TLS params.Method: refined / Origin x: 16.9965698696 Å / Origin y: -13.3318236835 Å / Origin z: -8.8799260354 Å
111213212223313233
T0.238428327064 Å20.0172101737317 Å28.32913196561E-6 Å2-0.209479672901 Å20.0176057458537 Å2--0.196047766574 Å2
L2.48322434133 °2-0.116006978683 °2-0.673750179311 °2-2.91564528199 °2-0.0809794688821 °2--2.1859526439 °2
S0.093162239783 Å °0.0687028177422 Å °0.0828415304816 Å °-0.030649792494 Å °-0.0916300773002 Å °-0.18122940492 Å °0.0489000848857 Å °0.0440871906535 Å °0.00588948793938 Å °
Refinement TLS groupSelection details: all

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