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- PDB-5gx9: PYP mutant - E46Q -

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Basic information

Entry
Database: PDB / ID: 5gx9
TitlePYP mutant - E46Q
ComponentsPhotoactive yellow protein
KeywordsSIGNALING PROTEIN / pas / lov / photoreceptor / light sensor / lbhb / shb / chromophore / photoreceptor protein / receptor / sensory transduction
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
DEUTERATED WATER / 4'-HYDROXYCINNAMIC ACID / Photoactive yellow protein
Similarity search - Component
Biological speciesHalorhodospira halophila (bacteria)
MethodNEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.493 Å
AuthorsYonezawa, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japanese Ministry of Education, Culture, Sports, Science and Technology25102003 Japan
CitationJournal: Sci Rep / Year: 2017
Title: Neutron crystallography of photoactive yellow protein reveals unusual protonation state of Arg52 in the crystal
Authors: Yonezawa, K. / Shimizu, N. / Kurihara, K. / Yamazaki, Y. / Kamikubo, H. / Kataoka, M.
History
DepositionSep 16, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.2Nov 28, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)14,0522
Polymers13,8881
Non-polymers1641
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6180 Å2
ΔGint26 kcal/mol
Surface area7150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.823, 66.823, 40.982
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Photoactive yellow protein / PYP


Mass: 13887.591 Da / Num. of mol.: 1 / Mutation: E46Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halorhodospira halophila (bacteria) / Gene: pyp / Plasmid: pET16b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9
Details: AMMONIUM SULPHATE, SODIUM CHLORIDE, SODIUM DIDEUTERIUM PHOSPHATE, DISODIUM DEUTERIUM PHOSPHATE, pH 9.0, VAPOR DIFFUSION, HANGING DROP, MICROSEEDING, temperature 295K

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: NUCLEAR REACTOR / Site: JRR-3M / Beamline: 1G-B / Wavelength: 2.6 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Jan 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: neutron
Radiation wavelengthWavelength: 2.6 Å / Relative weight: 1
ReflectionResolution: 1.493→100 Å / Num. obs: 15995 / % possible obs: 93.5 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 7.78
Reflection shellResolution: 1.493→1.55 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 2.4 / % possible all: 85.7

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Processing

Software
NameVersionClassification
PHENIX(1.12rc1_2815)refinement
AMoREmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OTA

1ota


Resolution: 1.493→33.445 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 18.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1996 1610 10.07 %RANDOM
Rwork0.1581 ---
obs0.1623 15983 93.48 %-
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.493→33.445 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms976 0 11 80 1067
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.0072326
NEUTRON DIFFRACTIONf_angle_d1.2334018
NEUTRON DIFFRACTIONf_dihedral_angle_d19.218609
NEUTRON DIFFRACTIONf_chiral_restr0.086155
NEUTRON DIFFRACTIONf_plane_restr0.01419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.493-1.54120.32831350.26331184NEUTRON DIFFRACTION86
1.5412-1.59630.26121400.23141239NEUTRON DIFFRACTION89
1.5963-1.66020.27151340.23071214NEUTRON DIFFRACTION89
1.6602-1.73580.2341450.19811273NEUTRON DIFFRACTION91
1.7358-1.82730.2491430.17941317NEUTRON DIFFRACTION94
1.8273-1.94170.19991470.15571333NEUTRON DIFFRACTION95
1.9417-2.09160.18241440.13911318NEUTRON DIFFRACTION96
2.0916-2.30210.18391550.12971354NEUTRON DIFFRACTION96
2.3021-2.63510.18021490.12651373NEUTRON DIFFRACTION98
2.6351-3.31940.17011540.13931369NEUTRON DIFFRACTION97
3.3194-33.45330.14441640.12341399NEUTRON DIFFRACTION97

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