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- PDB-7spv: Crystal structure of photoactive yellow protein (PYP); F92oCNF co... -

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Basic information

Entry
Database: PDB / ID: 7spv
TitleCrystal structure of photoactive yellow protein (PYP); F92oCNF 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 domain / Beta-Lactamase / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
4'-HYDROXYCINNAMIC ACID / Photoactive yellow protein
Similarity search - Component
Biological speciesHalorhodospira halophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 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
DepositionNov 3, 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

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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
Water2,000111
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)40.877, 40.877, 117.486
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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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.: 111 / 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: 2.02 Å3/Da / Density % sol: 39.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20 mM potassium phosphate, pH 6.0, 1 M NaCl; 2.0 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 X 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: 1.18→39.16 Å / Num. obs: 36561 / % possible obs: 99.1 % / Redundancy: 42 % / Biso Wilson estimate: 14.64 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.013 / Rrim(I) all: 0.085 / Net I/σ(I): 23.3 / Num. measured all: 1534716 / Scaling rejects: 390
Reflection shellResolution: 1.18→1.2 Å / Redundancy: 31.5 % / Rmerge(I) obs: 3.734 / Num. measured all: 46743 / Num. unique obs: 1485 / CC1/2: 0.685 / Rpim(I) all: 0.659 / Rrim(I) all: 3.795 / Net I/σ(I) obs: 1.3 / % possible all: 82

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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: 1.18→35.4 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.189 1814 4.98 %
Rwork0.165 34631 -
obs0.166 36445 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 47.3 Å2 / Biso mean: 18.72 Å2 / Biso min: 9.44 Å2
Refinement stepCycle: final / Resolution: 1.18→35.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms970 0 11 111 1092
Biso mean--12.67 28.44 -
Num. residues----124
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.18-1.210.30361290.23962551268096
1.21-1.250.2381370.199826852822100
1.25-1.290.22671380.190426692807100
1.29-1.330.23111420.186726582800100
1.33-1.380.18851430.1826572800100
1.39-1.450.20711390.15926762815100
1.45-1.520.18671400.150726762816100
1.52-1.620.17821400.147926502790100
1.62-1.740.18381410.149326832824100
1.74-1.920.17481400.159226702810100
1.92-2.20.17911390.156426702809100
2.2-2.770.21141440.178926752819100
2.77-35.40.17361420.161527112853100

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