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- PDB-1ts0: Structure of the pB1 intermediate from time-resolved Laue crystal... -

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Basic information

Entry
Database: PDB / ID: 1ts0
TitleStructure of the pB1 intermediate from time-resolved Laue crystallography
ComponentsPhotoactive yellow protein
Keywordsphotoreceptor
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 / Difference Fourier / Resolution: 1.6 Å
AuthorsIhee, H. / Rajagopal, S. / Srajer, V. / Pahl, R. / Anderson, S. / Schmidt, M. / Schotte, F. / Anfinrud, P.A. / Wulff, M. / Moffat, K.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Visualizing reaction pathways in photoactive yellow protein from nanoseconds to seconds.
Authors: Ihee, H. / Rajagopal, S. / Srajer, V. / Pahl, R. / Anderson, S. / Schmidt, M. / Schotte, F. / Anfinrud, P.A. / Wulff, M. / Moffat, K.
History
DepositionJun 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 9, 2015Group: Other
Revision 1.4Oct 11, 2017Group: Refinement description / Category: refine / software
Item: _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_obs / _software.name

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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
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.833, 66.833, 40.947
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Number of models2

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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 / Production host: Escherichia coli (E. coli) / References: UniProt: P16113
#2: Chemical ChemComp-HC4 / 4'-HYDROXYCINNAMIC ACID / PARA-COUMARIC ACID / P-Coumaric acid


Mass: 164.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8O3

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.6 M ammonium sulfate, 50 mM sodium phosphate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 13891 / Num. obs: 13891 / % possible obs: 100 %

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Processing

Software
NameClassification
LaueViewdata reduction
SHELXL-97refinement
LaueViewdata scaling
RefinementMethod to determine structure: Difference Fourier / Resolution: 1.6→30 Å / σ(F): 0
RfactorNum. reflection
Rfree0.1155 -
Rwork0.1087 -
all0.1166 13891
obs0.1166 13891
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms976 0 11 0 987

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