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- PDB-2pyp: PHOTOACTIVE YELLOW PROTEIN, PHOTOSTATIONARY STATE, 50% GROUND STA... -

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Basic information

Entry
Database: PDB / ID: 2pyp
TitlePHOTOACTIVE YELLOW PROTEIN, PHOTOSTATIONARY STATE, 50% GROUND STATE, 50% BLEACHED
ComponentsPHOTOACTIVE YELLOW PROTEIN
KeywordsPHOTORECEPTOR / CHROMOPHORE / LIGHT SENSOR FOR 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: 1.9 Å
AuthorsGenick, U.K. / Borgstahl, G.E.O. / Ng, K. / Ren, Z. / Pradervand, C. / Burke, P. / Srajer, V. / Teng, T. / Schildkamp, W. / Mcree, D.E. ...Genick, U.K. / Borgstahl, G.E.O. / Ng, K. / Ren, Z. / Pradervand, C. / Burke, P. / Srajer, V. / Teng, T. / Schildkamp, W. / Mcree, D.E. / Moffat, K. / Getzoff, E.D.
CitationJournal: Science / Year: 1997
Title: Structure of a protein photocycle intermediate by millisecond time-resolved crystallography.
Authors: Genick, U.K. / Borgstahl, G.E. / Ng, K. / Ren, Z. / Pradervand, C. / Burke, P.M. / Srajer, V. / Teng, T.Y. / Schildkamp, W. / McRee, D.E. / Moffat, K. / Getzoff, E.D.
History
DepositionFeb 3, 1997Processing site: BNL
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other / Refinement description
Category: pdbx_database_status / software ...pdbx_database_status / software / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site / _software.name

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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
Water1,00956
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.900, 66.900, 40.800
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 /


Mass: 13888.575 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halorhodospira halophila (bacteria) / Strain: BN9626 / 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.: 56 / 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: 1.88 Å3/Da / Density % sol: 35 %
Description: THE MODEL OF THE GROUND STATE STRUCTURE WAS USED
Crystal growpH: 4.8 / Details: pH 4.8
Crystal
*PLUS
Crystal grow
*PLUS
Method: unknown
Details: used to seeding, G. E. O. Borgstahl, (1995) Biochemistry, 34, 6278.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
22.5 M1dropNH4SO4
320 mMsodium phosphate1drop
42.5 M1reservoirNH4SO4

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Data collection

DiffractionMean temperature: 261 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 0.7 / Wavelength: 0.7, 2.0
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Jun 1, 1993
RadiationMonochromator: ALUMINUM FOIL 150 MICRON / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.71
221
ReflectionResolution: 1.9→10 Å / Num. obs: 10354 / % possible obs: 92.3 % / Redundancy: 5.5 %
Reflection shellResolution: 1.9→2.1 Å / % possible all: 86
Reflection
*PLUS
Num. measured all: 56947 / Rmerge(I) obs: 0.094

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
LaueViewdata reduction
LaueViewdata scaling
X-PLOR3.1phasing
RefinementResolution: 1.9→10 Å / σ(F): 3
RfactorNum. reflection% reflection
Rwork0.204 --
obs0.204 7392 89.3 %
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1072 0 11 56 1139
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.605
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.9→1.99 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rwork0.28 765 -
obs--74.34 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPH19.PEP
X-RAY DIFFRACTION2

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