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- PDB-7spx: Crystal structure of photoactive yellow protein (PYP); F28oCNF co... -

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Basic information

Entry
Database: PDB / ID: 7spx
TitleCrystal structure of photoactive yellow protein (PYP); F28oCNF 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: 0.97 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

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
Water1,964109
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)66.028, 66.028, 40.637
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.: 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: 1.82 Å3/Da / Density % sol: 32.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20 mM potassium phosphate, pH 6.0, 1 M NaCl; 2.2 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: 0.7749 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 0.97→40.64 Å / Num. obs: 59975 / % possible obs: 99.2 % / Redundancy: 13.1 % / Biso Wilson estimate: 7.68 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.023 / Rrim(I) all: 0.084 / Net I/σ(I): 17.6 / Num. measured all: 784978 / Scaling rejects: 107
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
0.97-0.989.51.8132343324740.5530.5911.9111.283.1
5.29-40.6414.10.025568840310.0070.02683.899.8

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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: 0.97→33.12 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 15.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1663 3059 5.11 %
Rwork0.1435 56817 -
obs0.1446 59876 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 41.77 Å2 / Biso mean: 11.6606 Å2 / Biso min: 4.5 Å2
Refinement stepCycle: final / Resolution: 0.97→33.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms970 0 11 109 1090
Biso mean--6.05 22.08 -
Num. residues----124
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 (%)
0.97-0.980.30321160.27442051216779
0.98-10.25621220.236926032725100
1-1.010.19771190.196926292748100
1.01-1.030.21791330.178125932726100
1.03-1.050.20021430.154625712714100
1.05-1.070.15021590.140825892748100
1.07-1.10.13411430.128925962739100
1.1-1.120.16661490.119225972746100
1.12-1.150.15281440.12325702714100
1.15-1.180.1521380.118726052743100
1.18-1.220.13651440.12325902734100
1.22-1.260.1531580.116925902748100
1.26-1.30.1471130.120326192732100
1.3-1.350.13861440.120226102754100
1.35-1.420.14821390.12626052744100
1.42-1.490.15471470.123326032750100
1.49-1.580.13581440.1326032747100
1.58-1.710.14111650.125125902755100
1.71-1.880.15421390.149526172756100
1.88-2.150.18271610.140326102771100
2.15-2.710.1885990.162126772776100
2.71-33.120.17751400.152926992839100

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