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- PDB-1s1y: Photoactivated chromophore conformation in Photoactive Yellow Pro... -

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Basic information

Entry
Database: PDB / ID: 1s1y
TitlePhotoactivated chromophore conformation in Photoactive Yellow Protein (E46Q mutant) from 10 microseconds to 3 milliseconds
ComponentsPhotoactive yellow protein
KeywordsPHOTORECEPTOR / room temperature / time-resolved
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: 1.6 Å
AuthorsAnderson, S. / Srajer, V. / Pahl, R. / Rajagopal, S. / Schotte, F. / Anfinrud, P. / Wulff, M. / Moffat, K.
CitationJournal: Structure / Year: 2004
Title: Chromophore conformation and the evolution of tertiary structural changes in photoactive yellow protein
Authors: Anderson, S. / Srajer, V. / Pahl, R. / Rajagopal, S. / Schotte, F. / Anfinrud, P. / Wulff, M. / Moffat, K.
History
DepositionJan 7, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _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)14,0522
Polymers13,8881
Non-polymers1641
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.917, 66.917, 41.002
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 / Production host: Escherichia coli (E. coli) / 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.: 111 / 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: 15

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Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: ammonium sulfate, sodium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12881
22881
32881
42881
Diffraction source
SourceSiteBeamlineID
SYNCHROTRONAPS 14-ID-B1
SYNCHROTRONAPS 14-ID-B2
SYNCHROTRONAPS 14-ID-B3
SYNCHROTRONESRF ID094
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDMar 23, 2001
MARRESEARCH2IMAGE PLATESep 20, 2001
MARRESEARCH3CCDDec 19, 2001
MARRESEARCH4CCDDec 6, 2001
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1LAUELneutron1
2LAUELneutron1
3LAUELneutron1
4LAUELneutron1
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.6→100 Å / Num. obs: 13371 / % possible obs: 95.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.6→1.67 Å / % possible all: 83.8

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Processing

Software
NameClassification
LaueViewdata scaling
LaueViewdata reduction
XTALVIEWrefinement
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→100 Å / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: Engh & Huber / Details: difference refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.0702 669 -random
Rwork0.0639 ---
all0.0664 13371 --
obs0.0655 13201 95.8 %-
Refinement stepCycle: LAST / Resolution: 1.6→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1222 0 26 111 1359

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