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- PDB-7sjj: Crystal structure of photoactive yellow protein (PYP); F96oCNF co... -

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Basic information

Entry
Database: PDB / ID: 7sjj
TitleCrystal structure of photoactive yellow protein (PYP); F96oCNF construct
ComponentsPhotoactive yellow protein
KeywordsSIGNALING PROTEIN / PHOTORECEPTOR
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: 0.95 Å
AuthorsWeaver, J.B. / Kirsh, J.M. / Boxer, S.G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)2R35GM11804406 United States
National Science Foundation (NSF, United States)1915727 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: Nitrile Infrared Intensities Characterize Electric Fields and Hydrogen Bonding in Protic, Aprotic, and Protein Environments.
Authors: Weaver, J.B. / Kozuch, J. / Kirsh, J.M. / Boxer, S.G.
History
DepositionOct 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: 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
Revision 1.2Aug 17, 2022Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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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)14,0782
Polymers13,9141
Non-polymers1641
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.164, 66.164, 40.896
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: 13913.585 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 str. K-12 substr. DH10B (bacteria)
Strain (production host): DH10B / 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.: 124 / 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: 1.84 Å3/Da / Density % sol: 33.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20 mM potassium phosphate, pH 6.0, 1 M NaCl; 2.1 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.7126 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7126 Å / Relative weight: 1
ReflectionResolution: 0.95→33.29 Å / Num. obs: 61787 / % possible obs: 97.2 % / Redundancy: 41.2 % / Biso Wilson estimate: 8.36 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.018 / Rrim(I) all: 0.116 / Net I/σ(I): 17.9 / Num. measured all: 2546198 / Scaling rejects: 462
Reflection shellResolution: 0.95→0.97 Å / Redundancy: 22.7 % / Rmerge(I) obs: 3.012 / Num. measured all: 49902 / Num. unique obs: 2194 / CC1/2: 0.456 / Rpim(I) all: 0.62 / Rrim(I) all: 3.081 / Net I/σ(I) obs: 1.2 / % possible all: 69.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NWZ

1nwz


Resolution: 0.95→33.29 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.159 3084 5 %
Rwork0.139 58645 -
obs0.14 61729 97.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 36.7 Å2 / Biso mean: 12.22 Å2 / Biso min: 3.65 Å2
Refinement stepCycle: final / Resolution: 0.95→33.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms978 0 11 126 1115
Biso mean--6.83 19.34 -
Num. residues----125
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
0.95-0.970.32981020.29881844194668
0.97-0.980.28341370.2572684282197
0.98-10.25231450.21372633277897
1-1.020.21991430.17652659280298
1.02-1.040.19451410.15982664280598
1.04-1.060.19031420.14292603274597
1.06-1.080.15971370.13692727286498
1.08-1.110.14211430.10972677282098
1.11-1.140.13411410.10942670281198
1.14-1.170.11211400.10552694283499
1.17-1.20.10311420.0962700284299
1.2-1.240.11741400.10382693283399
1.24-1.280.13471400.10142698283899
1.28-1.340.14951430.11362732287599
1.34-1.40.14141410.11152739288099
1.4-1.470.13121460.11882693283998
1.47-1.560.1471400.1192712285299
1.56-1.680.13741470.121927372884100
1.68-1.850.14311410.139127572898100
1.85-2.120.15891430.145327382881100
2.12-2.670.17691420.1652766290899
2.67-33.290.17611480.151628252973100

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