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- PDB-8e1k: Crystal structure of photoactive yellow protein (PYP); F96oCNF M1... -

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Basic information

Entry
Database: PDB / ID: 8e1k
TitleCrystal structure of photoactive yellow protein (PYP); F96oCNF M100Q 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: 1.02 Å
AuthorsKirsh, J.M. / Weaver, J.B. / 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: To Be Published
Title: Protic and Aprotic Interactions Systematically Perturbed and Mapped via MD and IR Spectroscopy
Authors: Kirsh, J.M. / Kozuch, J. / Weaver, J.B. / Boxer, S.G.
History
DepositionAug 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 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)14,0752
Polymers13,9111
Non-polymers1641
Water1,78399
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)66.362, 66.362, 40.574
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: 13910.518 Da / Num. of mol.: 1 / Mutation: M100Q
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 33.03 %
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: 1.02→40.57 Å / Num. obs: 50719 / % possible obs: 98.9 % / Redundancy: 41 % / Biso Wilson estimate: 10.66 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.019 / Rrim(I) all: 0.124 / Net I/σ(I): 16.1 / Num. measured all: 2080017 / Scaling rejects: 215
Reflection shellResolution: 1.02→1.04 Å / Redundancy: 24.1 % / Rmerge(I) obs: 3.387 / Num. measured all: 47202 / Num. unique obs: 1956 / CC1/2: 0.463 / Rpim(I) all: 0.68 / Rrim(I) all: 3.46 / Net I/σ(I) obs: 1.1 / % possible all: 77

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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: 1.02→33.18 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.161 2527 4.99 %
Rwork0.147 48112 -
obs0.148 50639 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 53.03 Å2 / Biso mean: 15.18 Å2 / Biso min: 7.44 Å2
Refinement stepCycle: final / Resolution: 1.02→33.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms971 0 11 100 1082
Biso mean--8.66 22.11 -
Num. residues----124
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.02-1.040.34161140.28492132224680
1.04-1.070.21531430.217426942837100
1.07-1.090.21551340.172326842818100
1.09-1.110.16871450.149426792824100
1.11-1.140.15391390.131327082847100
1.14-1.170.15541440.12426862830100
1.17-1.210.1481430.122426942837100
1.21-1.250.14051390.121626722811100
1.25-1.290.13821400.11327142854100
1.29-1.340.15921420.121926912833100
1.34-1.40.13911450.119226992844100
1.4-1.480.1531420.123627062848100
1.48-1.570.14981390.123526962835100
1.57-1.690.14951430.127727362879100
1.69-1.860.1651400.140526712811100
1.86-2.130.1631450.1527342879100
2.13-2.680.16521460.169927372883100
2.68-33.180.16131440.156727792923100

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