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- PDB-1d7e: CRYSTAL STRUCTURE OF THE P65 CRYSTAL FORM OF PHOTOACTIVE YELLOW P... -

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Basic information

Entry
Database: PDB / ID: 1d7e
TitleCRYSTAL STRUCTURE OF THE P65 CRYSTAL FORM OF PHOTOACTIVE YELLOW PROTEIN
ComponentsPHOTOACTIVE YELLOW PROTEIN
KeywordsPHOTOSYNTHESIS / PHOTORECEPTOR
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: 1.39 Å
AuthorsVan Aalten, D.M.F. / Crielaard, W. / Hellingwerf, K.J. / Joshua-Tor, L.
Citation
Journal: Protein Sci. / Year: 2000
Title: Conformational substates in different crystal forms of the photoactive yellow protein--correlation with theoretical and experimental flexibility.
Authors: van Aalten, D.M. / Crielaard, W. / Hellingwerf, K.J. / Joshua-Tor, L.
#1: Journal: Biochemistry / Year: 1995
Title: 1.4 A structure of photoactive yellow protein, a cytosolic photoreceptor: unusual fold, active site, and chromophore.
Authors: Borgstahl, G.O. / Williams, D.R. / Getzoff, E.D.
#2: Journal: Biochemistry / Year: 1998
Title: Solution structure and backbone dynamics of the photoactive yellow protein.
Authors: Dux, P. / Rubinstenn, G. / Vuister, G.W. / Boelens, R. / Mulder, F.A.A.
History
DepositionOct 17, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification / _software.name
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _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)13,6542
Polymers13,4901
Non-polymers1641
Water2,720151
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.561, 40.561, 118.089
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein PHOTOACTIVE YELLOW PROTEIN / / PYP


Mass: 13490.118 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halorhodospira halophila (bacteria) / Plasmid: PHISP / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / 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.: 151 / 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: 2.02 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 2K, MES., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 17K
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Details: used as seeds, Borgstahl, G.O., (1995) Biochemistry, 34, 6278.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13.2 M1reservoirNH4SO4
220 mMsodium phosphate1reservoir
315 mg/mlprotein1drop
42.5 M1dropNH4SO4
520 mMsodium phosphate1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.39→15 Å / Num. all: 194171 / Num. obs: 194171 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 8.9 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 23.1
Reflection shellResolution: 1.39→1.44 Å / Rmerge(I) obs: 0.126 / % possible all: 100
Reflection
*PLUS
Highest resolution: 1.39 Å / Lowest resolution: 15 Å / Num. obs: 21796 / Observed criterion σ(I): -3 / Redundancy: 8.9 % / Num. measured all: 194171
Reflection shell
*PLUS
% possible obs: 100 % / Num. unique obs: 2190 / Mean I/σ(I) obs: 21.3

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Processing

Software
NameClassification
AMoREphasing
SHELXL-97refinement
MAR345data collection
SCALEPACKdata scaling
RefinementResolution: 1.39→8 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER (IN SHELX)
RfactorNum. reflection% reflectionSelection details
Rfree0.198 1041 5 %RANDOM
Rwork0.139 ---
obs0.139 20594 100 %-
all-20594 --
Refinement stepCycle: LAST / Resolution: 1.39→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms942 0 11 211 1164
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d1.92
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.139 / Rfactor obs: 0.138 / Rfactor Rwork: 0.139
Solvent computation
*PLUS
Displacement parameters
*PLUS

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