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- PDB-4bbt: The PR1 Photocycle Intermediate of Photoactive Yellow Protein -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4bbt
TitleThe PR1 Photocycle Intermediate of Photoactive Yellow Protein
ComponentsPHOTOACTIVE YELLOW PROTEIN
KeywordsSIGNALING PROTEIN / PHOTORECEPTOR / LIGHT SENSOR / CHROMOPHORE / PHOTORECEPTOR PROTEIN / RECEPTOR / SENSORY TRANSDUCTION / PAS / LOV
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 / OTHER / Resolution: 1.6 Å
AuthorsSchotte, F. / Cho, H.S. / Kaila, V.R.I. / Kamikubo, H. / Dashdorj, N. / Henry, E.R. / Graber, T.J. / Henning, R. / Wulff, M. / Hummer, G. ...Schotte, F. / Cho, H.S. / Kaila, V.R.I. / Kamikubo, H. / Dashdorj, N. / Henry, E.R. / Graber, T.J. / Henning, R. / Wulff, M. / Hummer, G. / Kataoka, M. / Anfinrud, P.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Watching a Signaling Protein Function in Real Time Via 100-Ps Time-Resolved Laue Crystallography.
Authors: Schotte, F. / Cho, H.S. / Kaila, V.R.I. / Kamikubo, H. / Dashdorj, N. / Henry, E.R. / Graber, T.J. / Henning, R. / Wulff, M. / Hummer, G. / Kataoka, M. / Anfinrud, P.A.
History
DepositionSep 27, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references
Revision 1.2Jan 25, 2017Group: Data collection
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp

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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
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.833, 66.833, 40.947
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) / Plasmid: PET16B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / 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.: 139 / 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: 3

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Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35.24 % / Description: NONE
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 2.2 M AMMONIUM SULFATE, 1.0 M SODIUM CHLORIDE, AND 10 MM SODIUM DIDEUTERIUM PHOSPHATE, 10 MM DISODIUM DEUTERIUM PHOSPHATE, PH 9.0, VAPOUR DIFFUSION, HANGING DROP, MICROSEEDING, TEMPERATURE 295 K

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.96-1.30
DetectorType: MARRESEARCH SX-165 / Detector: CCD / Date: Mar 12, 2011 / Details: MIRRORS
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.961
21.31
ReflectionResolution: 1.6→13.28 Å / Num. obs: 10605 / % possible obs: 59 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Biso Wilson estimate: 13.82 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 6.9
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 0.9 / % possible all: 19

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.6→13.285 Å / SU ML: 0.36 / σ(F): 0 / Phase error: 27.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2277 416 4.1 %
Rwork0.1693 --
obs0.1717 10262 74 %
Solvent computationShrinkage radii: 0 Å / VDW probe radii: 0 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 9.316 Å2 / ksol: 0.101 e/Å3
Displacement parametersBiso mean: 23.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.5199 Å20 Å20 Å2
2--0.5199 Å20 Å2
3----1.0397 Å2
Refinement stepCycle: LAST / Resolution: 1.6→13.285 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms976 0 11 139 1126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071009
X-RAY DIFFRACTIONf_angle_d1.2071359
X-RAY DIFFRACTIONf_dihedral_angle_d14.058367
X-RAY DIFFRACTIONf_chiral_restr0.082140
X-RAY DIFFRACTIONf_plane_restr0.005180
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6001-1.83120.4405980.33152497X-RAY DIFFRACTION57
1.8312-2.30510.24831610.21153665X-RAY DIFFRACTION82
2.3051-13.28510.17951570.12063684X-RAY DIFFRACTION82

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