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- PDB-1uwp: Initial Events in the Photocycle of Photoactive Yellow Protein -

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Basic information

Entry
Database: PDB / ID: 1uwp
TitleInitial Events in the Photocycle of Photoactive Yellow Protein
ComponentsPHOTOACTIVE YELLOW PROTEIN
KeywordsSIGNALING PROTEIN / PAS / LOV / GAF / DOMAINS / FOLD PHOTOCYCLE / PHOTOACTIVE / PHOTORECEPTOR / YELLOW
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 / MAD / Resolution: 1.2 Å
AuthorsKort, R. / Hellingwerf, K.J. / Ravelli, R.B.G.
Citation
Journal: J. Biol. Chem. / Year: 2004
Title: Initial events in the photocycle of photoactive yellow protein.
Authors: Kort, R. / Hellingwerf, K.J. / Ravelli, R.B.
#1: Journal: Photochem.Photobiol. / Year: 2003
Title: Characterization of Photocycle Intermediates in Crystalline Photoactive Yellow Protein
Authors: Kort, R. / Ravelli, R.B.G. / Schotte, F. / Bourgeois, D. / Crielaard, W. / Hellingwerf, K.J. / Wulff, M.
History
DepositionFeb 11, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Version format compliance
Revision 1.2Jan 30, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _exptl_crystal_grow.method
Revision 1.3Feb 27, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation
Category: citation / citation_author ...citation / citation_author / exptl_crystal_grow / pdbx_database_proc / struct_biol / struct_conn
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _exptl_crystal_grow.temp / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: PHOTOACTIVE YELLOW PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4794
Polymers14,1231
Non-polymers3563
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)65.922, 65.922, 40.584
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
11X-1128-

SO4

21X-2016-

HOH

31X-2017-

HOH

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Components

#1: Protein PHOTOACTIVE YELLOW PROTEIN / PYP


Mass: 14123.052 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: LIGHT STATE / Source: (gene. exp.) HALORHODOSPIRA HALOPHILA (bacteria) / Strain: BN9626
Description: HALORHODOSPIRA HALOPHILA PREVIOUSLY KNOWN AS ECTOTHIORHODOSPIRA HALOPHILA
Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15/ PREP4 PHISP / 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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE MET-RESIDUES WERE SUBSTITUTED BY SEMET

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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: 1.72 Å3/Da / Density % sol: 20 %
Description: STATISTICS ARE GIVEN FOR REMOTE DATA SET (2 SWEEPS)
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.25 M NH4SO4, 20 MM SODIUM PHOSPHATE PH 7, VAPOR DIFFUSION, HANGING DROP, TEMP 298K

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Data collection

DiffractionMean temperature: 85 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393,0.9796
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 30, 2002 / Details: BENT MIRROR
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.93931
20.97961
ReflectionResolution: 1.2→30 Å / Num. obs: 146753 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 14.6
Reflection shellResolution: 1.2→1.23 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.199 / Mean I/σ(I) obs: 4.5 / % possible all: 94.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.2→40 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.972 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. AN EARLY INTERMEDIATE OF THE PHOTOCYCLE OF PYP WAS DETERMINED BY THE DATA COLLECTION OF 2 MAD DATA SETS ON ONE CRYSTAL OF PYP. THE FIRST ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. AN EARLY INTERMEDIATE OF THE PHOTOCYCLE OF PYP WAS DETERMINED BY THE DATA COLLECTION OF 2 MAD DATA SETS ON ONE CRYSTAL OF PYP. THE FIRST MAD DATA SET WAS OBTAINED IN THE DARK, WHEREAS THE CRYSTAL WAS ILLUMINATED FOR THE SECOND DATA SET. DATA WERE CORRECTED FOR MINOR RADIATION DAMAGE USING 2 OTHER MAD DATA SETS, COLLECTED ON AN ISOMORPHOUS CRYSTAL THAT WAS KEPT IN THE DARK. THE SAME CRYSTAL WAS USED FOR PDB- ID 1UWN.
RfactorNum. reflection% reflectionSelection details
Rfree0.157 1559 5 %RANDOM
Rwork0.136 ---
obs0.137 29323 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 10.61 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å2-0.08 Å20 Å2
2---0.16 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms970 0 21 138 1129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221237
X-RAY DIFFRACTIONr_bond_other_d00.0211051
X-RAY DIFFRACTIONr_angle_refined_deg1.9792.0211661
X-RAY DIFFRACTIONr_angle_other_deg4.01732495
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5865145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1130.2168
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021363
X-RAY DIFFRACTIONr_gen_planes_other0.0360.02260
X-RAY DIFFRACTIONr_nbd_refined0.4320.2604
X-RAY DIFFRACTIONr_nbd_other0.2920.21307
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1980.21085
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.2116
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.260
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2850.292
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2660.235
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.461.5719
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.2121164
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8163518
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0844.5495
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.2→1.23 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.229 107
Rwork0.238 2052

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