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- PDB-9cgh: Photoactive yellow protein crystallized in situ on cyclic olefin ... -

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Basic information

Entry
Database: PDB / ID: 9cgh
TitlePhotoactive yellow protein crystallized in situ on cyclic olefin copolymer microfluidic chip through counter diffusion
ComponentsPhotoactive yellow protein
KeywordsPHOTOSYNTHESIS / P65
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: 1.32 Å
AuthorsLiu, Z. / Gu, K.K. / Shelby, M.L. / Roy, D. / Muniyappan, S. / Schmidt, M. / Narayanasamy, S.R. / Coleman, M.A. / Frank, M. / Kuhl, T.L.
Funding support United States, 5items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1231306 United States
National Science Foundation (NSF, United States)2153503 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM117342 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI144184 United States
Department of Energy (DOE, United States)P30GM133894 United States
CitationJournal: To Be Published
Title: Photoactive yellow protein crystallized in situ on cyclic olefin copolymer microfluidic chip through counter diffusion
Authors: Liu, Z. / Gu, K.K. / Shelby, M.L. / Roy, D. / Muniyappan, S. / Schmidt, M. / Narayanasamy, S.R. / Coleman, M.A. / Frank, M. / Kuhl, T.L.
History
DepositionJun 28, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release

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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
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.194, 41.194, 117.819
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.08 Å3/Da / Density % sol: 40.8 %
Crystal growTemperature: 293 K / Method: counter-diffusion / Details: PEG 4000, 2-Morpholinoethanesulphonic acid

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.32→35.68 Å / Num. obs: 26412 / % possible obs: 99.64 % / Redundancy: 13.8 % / CC1/2: 0.999 / Net I/σ(I): 23
Reflection shellResolution: 1.32→1.34 Å / Num. unique obs: 1232 / CC1/2: 0.437 / % possible all: 93.26

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Processing

Software
NameVersionClassification
PHENIX1.19.2refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.32→35.68 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 19.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.179 2013 7.64 %
Rwork0.1709 --
obs0.1715 26336 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.32→35.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms968 0 11 72 1051
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071057
X-RAY DIFFRACTIONf_angle_d0.9491412
X-RAY DIFFRACTIONf_dihedral_angle_d6.24135
X-RAY DIFFRACTIONf_chiral_restr0.091142
X-RAY DIFFRACTIONf_plane_restr0.006185
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.32-1.350.27031380.23271633X-RAY DIFFRACTION94
1.35-1.390.24441350.21321725X-RAY DIFFRACTION98
1.39-1.430.21091430.20151750X-RAY DIFFRACTION100
1.43-1.480.22461410.18081734X-RAY DIFFRACTION100
1.48-1.530.20141480.18381777X-RAY DIFFRACTION100
1.53-1.590.18061430.17961724X-RAY DIFFRACTION100
1.59-1.660.20861500.17571741X-RAY DIFFRACTION100
1.66-1.750.18191390.17861729X-RAY DIFFRACTION100
1.75-1.860.19191500.17391754X-RAY DIFFRACTION100
1.86-20.19651440.17221738X-RAY DIFFRACTION100
2-2.210.1591430.16381748X-RAY DIFFRACTION100
2.21-2.520.17121450.16861758X-RAY DIFFRACTION100
2.53-3.180.18781460.18521762X-RAY DIFFRACTION100
3.18-35.680.15821480.15411750X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -17.0995 Å / Origin y: 14.1315 Å / Origin z: 0.2125 Å
111213212223313233
T0.133 Å20.0142 Å20.0113 Å2-0.1318 Å20.0104 Å2--0.1378 Å2
L1.6305 °2-0.1716 °2-0.4136 °2-1.2574 °2-0.062 °2--1.454 °2
S-0.045 Å °0.0146 Å °-0.1147 Å °0.1014 Å °0.0303 Å °0.103 Å °0.0604 Å °0.0181 Å °-0.0001 Å °
Refinement TLS groupSelection details: all

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