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

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Basic information

Entry
Database: PDB / ID: 8dzu
TitleCrystal structure of photoactive yellow protein (PYP); F96oCNF M100H 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: 1.04 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 8, 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)14,0852
Polymers13,9211
Non-polymers1641
Water1,910106
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)66.249, 66.249, 40.800
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: 13920.536 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.: 106 / 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: 33.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20 mM potassium phosphate, pH 6.0, 1 M NaCl; 2.5 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: 1.04→33.25 Å / Num. obs: 48038 / % possible obs: 98.6 % / Redundancy: 41.1 % / Biso Wilson estimate: 9.52 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.023 / Rrim(I) all: 0.151 / Net I/σ(I): 14.3 / Num. measured all: 1976427 / Scaling rejects: 1759
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
1.04-1.0619.32.8923270016900.5380.6472.971.170.8
5.71-33.2540.70.065133433280.9990.010.06651.699.8

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Processing

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

1nwz


Resolution: 1.04→33.12 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.161 2405 5.01 %
Rwork0.143 45577 -
obs0.1439 47982 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 45.87 Å2 / Biso mean: 13.3411 Å2 / Biso min: 3.06 Å2
Refinement stepCycle: final / Resolution: 1.04→33.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms972 0 11 107 1090
Biso mean--7.68 20.7 -
Num. residues----124
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.04-1.060.33161090.25252066217577
1.06-1.090.2421420.196926892831100
1.09-1.110.19921390.166327092848100
1.11-1.140.15861420.142327002842100
1.14-1.170.17951420.131627102852100
1.17-1.210.14011440.12627052849100
1.21-1.240.15771370.117127062843100
1.24-1.290.16141480.113927032851100
1.29-1.340.13461420.1127122854100
1.34-1.40.15491460.113927232869100
1.4-1.480.13731440.113827052849100
1.48-1.570.15591440.114627172861100
1.57-1.690.13871440.115227282872100
1.69-1.860.15621420.136927252867100
1.86-2.130.13491430.143127332876100
2.13-2.680.17571480.160827492897100
2.68-33.120.16641490.159827972946100

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