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- PDB-1f9i: CRYSTAL STRUCTURE OF THE PHOTOACTIVE YELLOW PROTEIN MUTANT Y42F -

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Basic information

Entry
Database: PDB / ID: 1f9i
TitleCRYSTAL STRUCTURE OF THE PHOTOACTIVE YELLOW PROTEIN MUTANT Y42F
ComponentsPHOTOACTIVE YELLOW PROTEIN
KeywordsSIGNALING PROTEIN / Photoreceptor / Light-Sensor for Negative Phototaxis
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 / Resolution: 1.1 Å
AuthorsBrudler, R. / Meyer, T.E. / Genick, U.K. / Tollin, G. / Getzoff, E.D.
CitationJournal: Biochemistry / Year: 2000
Title: Coupling of hydrogen bonding to chromophore conformation and function in photoactive yellow protein.
Authors: Brudler, R. / Meyer, T.E. / Genick, U.K. / Devanathan, S. / Woo, T.T. / Millar, D.P. / Gerwert, K. / Cusanovich, M.A. / Tollin, G. / Getzoff, E.D.
History
DepositionJul 10, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 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)14,0372
Polymers13,8731
Non-polymers1641
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.699, 65.699, 40.239
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-2078-

HOH

21A-2080-

HOH

31A-2097-

HOH

41A-2104-

HOH

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Components

#1: Protein PHOTOACTIVE YELLOW PROTEIN /


Mass: 13872.575 Da / Num. of mol.: 1 / Mutation: Y42F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halorhodospira halophila (bacteria) / Plasmid: PET 20B / 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 1.81 Å3/Da / Density % sol: 31.92 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: Ammonium Sulfate, HEPES, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K
Crystal grow
*PLUS
pH: 7 / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.5 Mammonium sulfate1reservoir
220 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 4, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.1→30 Å / Num. all: 186098 / Num. obs: 40647 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 4.6 % / Biso Wilson estimate: 9.4 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 24
Reflection shellResolution: 1.1→1.13 Å / Redundancy: 3 % / Rmerge(I) obs: 0.41 / % possible all: 99
Reflection
*PLUS
Num. measured all: 186098
Reflection shell
*PLUS
% possible obs: 99 % / Rmerge(I) obs: 0.39

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Processing

Software
NameClassification
XFITdata reduction
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.1→30 Å / σ(F): 2 / σ(I): 4 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.171 2003 RANDOM
Rwork0.127 --
all0.146 38062 -
obs0.144 30545 -
Refinement stepCycle: LAST / Resolution: 1.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms988 0 11 104 1103
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.035
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / σ(F): 2 / Rfactor obs: 0.127 / Rfactor Rwork: 0.144
Solvent computation
*PLUS
Displacement parameters
*PLUS

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