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- PDB-2zoi: Neutron Crystal Structure of Photoactive Yellow Protein, Wild typ... -

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Basic information

Entry
Database: PDB / ID: 2zoi
TitleNeutron Crystal Structure of Photoactive Yellow Protein, Wild type, at 295K
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: 1.5 Å
AuthorsYamaguchi, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Low-barrier hydrogen bond in photoactive yellow protein
Authors: Yamaguchi, S. / Kamikubo, H. / Kurihara, K. / Kuroki, R. / Niimura, N. / Shimizu, N. / Yamazaki, Y. / Kataoka, M.
History
DepositionMay 21, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)14,0532
Polymers13,8891
Non-polymers1641
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.145, 67.145, 41.119
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: 13888.575 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halorhodospira halophila (bacteria) / Gene: PYP / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / 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.: 73 / 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

Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop, microseeding / 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 / Wavelength: 2.6 / Wavelength: 2.6 Å
DetectorType: MACSCIENCE DIP SCANNER FOR NEUTRONS / Detector: IMAGE PLATE / Date: Mar 31, 2007
RadiationMonochromator: ELASTICALLY-BENT PERFECT SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.6 Å / Relative weight: 1
ReflectionResolution: 1.5→100 Å / Num. obs: 15293 / % possible obs: 89.6 % / Redundancy: 2.6 % / Biso Wilson estimate: 9.644 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 7.4
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 2.91 / Num. unique all: 1234 / % possible all: 72.8

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1.1refinement
MACSCIENCEDIPdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZOH

2zoh


Resolution: 1.5→70 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 150751.56 / Data cutoff low absF: 0 / Isotropic thermal model: Restrained Isotropic Thermal Model / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
Details: The DE2 (and HE2) atom of GLU A 46 is involved in the special type of hydrogen bond, so-called Low barrier hydrogen bond. In such hydrogen bond, the HE2 (or DE2) atom is shared by the two ...Details: The DE2 (and HE2) atom of GLU A 46 is involved in the special type of hydrogen bond, so-called Low barrier hydrogen bond. In such hydrogen bond, the HE2 (or DE2) atom is shared by the two donor atoms, which are OE2(GLU 46) and O4'(HC4 169) in this case. X-PLOR 3.851 WAS ALSO USED FOR THE REFINEMENT. THE STANDARD TOPOLOGY AND PARAMETER FILES WERE CHANGED FOR HYDROGEN AND DEUTERIUM ATOM PARAMETERS TO MEET THE REQUIREMENTS OF THE NEUTRON STRUCTURE REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.219 757 5 %RANDOM
Rwork0.192 ---
obs-15283 89.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 20.4728 Å2 / ksol: 0.05657634 e/Å3
Displacement parametersBiso mean: 14.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-50 Å
Luzzati sigma a0.21 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.5→70 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms976 0 11 73 1060
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
NEUTRON DIFFRACTIONc_bond_d0.013
NEUTRON DIFFRACTIONc_bond_d_na
NEUTRON DIFFRACTIONc_bond_d_prot
NEUTRON DIFFRACTIONc_angle_d
NEUTRON DIFFRACTIONc_angle_d_na
NEUTRON DIFFRACTIONc_angle_d_prot
NEUTRON DIFFRACTIONc_angle_deg1.7
NEUTRON DIFFRACTIONc_angle_deg_na
NEUTRON DIFFRACTIONc_angle_deg_prot
NEUTRON DIFFRACTIONc_dihedral_angle_d24.4
NEUTRON DIFFRACTIONc_dihedral_angle_d_na
NEUTRON DIFFRACTIONc_dihedral_angle_d_prot
NEUTRON DIFFRACTIONc_improper_angle_d1.68
NEUTRON DIFFRACTIONc_improper_angle_d_na
NEUTRON DIFFRACTIONc_improper_angle_d_prot
NEUTRON DIFFRACTIONc_mcbond_it2.781.5
NEUTRON DIFFRACTIONc_mcangle_it3.712
NEUTRON DIFFRACTIONc_scbond_it5.142
NEUTRON DIFFRACTIONc_scangle_it5.942.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.293 94 4.4 %
Rwork0.3 2049 -
obs-2049 75.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
NEUTRON DIFFRACTION1pyp_neutron_v11.parampyp_neutron_v11_D4.top
NEUTRON DIFFRACTION2water_neutron_v11.paramwater_neutron_v11.top

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