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- PDB-2zoh: X-ray Crystal Structure of Photoactive Yellow Protein, Wild type,... -

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Basic information

Entry
Database: PDB / ID: 2zoh
TitleX-ray Crystal Structure of Photoactive Yellow Protein, Wild type, at 295K
ComponentsPhotoactive yellow protein
KeywordsSIGNALING PROTEIN / PAS / LOV / PHOTORECEPTOR / LIGHT SENSOR / 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
4'-HYDROXYCINNAMIC ACID / Photoactive yellow protein
Similarity search - Component
Biological speciesHalorhodospira halophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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 20, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 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

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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
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.830, 66.830, 40.920
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O

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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: 1.9 Å3/Da / Density % sol: 35.24 %
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: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.45 / Wavelength: 0.45 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 3, 2006
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.45 Å / Relative weight: 1
ReflectionResolution: 1.25→57.83 Å / Num. all: 28967 / Num. obs: 28967 / % possible obs: 100 % / Redundancy: 11.1 % / Biso Wilson estimate: 10.11 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 21.9
Reflection shellResolution: 1.25→1.32 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 7.3 / Num. unique all: 4176 / Rsym value: 0.356 / % possible all: 100

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Processing

Software
NameVersionClassification
SHELXmodel building
SHELXL-97refinement
ADSCQuantumdata collection
XDSdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PHY

2phy


Resolution: 1.25→50 Å / Num. parameters: 10353 / Num. restraintsaints: 13011 / Isotropic thermal model: ANISOTROPIC / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1488 1448 5 %RANDOM
Rwork0.1122 ---
all-28950 --
obs-28950 100 %-
Refine analyzeNum. disordered residues: 10 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1107
Refinement stepCycle: LAST / Resolution: 1.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1019 0 11 120 1150
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0289
X-RAY DIFFRACTIONs_zero_chiral_vol0.08
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.116
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.031
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.042
X-RAY DIFFRACTIONs_approx_iso_adps0.104

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