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- PDB-2phy: PHOTOACTIVE YELLOW PROTEIN, DARK STATE (UNBLEACHED) -

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Basic information

Entry
Database: PDB / ID: 2phy
TitlePHOTOACTIVE YELLOW PROTEIN, DARK STATE (UNBLEACHED)
ComponentsPHOTOACTIVE YELLOW PROTEIN
KeywordsPHOTORECEPTOR / 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 / Resolution: 1.4 Å
AuthorsBorgstahl, G.E.O. / Getzoff, E.D.
Citation
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.E. / Williams, D.R. / Getzoff, E.D.
#1: Journal: Biochemistry / Year: 1994
Title: Complete Chemical Structure of Photoactive Yellow Protein: Novel Thioester-Linked 4-Hydroxycinnamyl Chromophore and Photocycle Chemistry
Authors: Baca, M. / Borgstahl, G.E.O. / Boissinot, M. / Burke, P.M. / Williams, D.R. / Slater, K.A. / Getzoff, E.D.
History
DepositionApr 12, 1995Processing site: BNL
SupersessionOct 15, 1995ID: 1PHY
Revision 1.0Oct 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX HELIX DETERMINATION METHOD: KABSCH AND SANDER ALGORITHM CHECKED BY HAND ON THE GRAPHICS DISPLAY.
Remark 700SHEET SHEET SHEET_ID: B-1; DETERMINATION METHOD: KABSCH AND SANDER ALGORITHM CHECKED BY HAND ON THE ...SHEET SHEET SHEET_ID: B-1; DETERMINATION METHOD: KABSCH AND SANDER ALGORITHM CHECKED BY HAND ON THE GRAPHICS DISPLAY.

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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
Water1,65792
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 / PYP


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


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.: 92 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCOMPND MOLECULE: PHOTOACTIVE YELLOW PROTEIN. 4-HYDROXYCINNAMYL CHROMOPHORE COVALENTLY LINKED TO ...COMPND MOLECULE: PHOTOACTIVE YELLOW PROTEIN. 4-HYDROXYCINNAMYL CHROMOPHORE COVALENTLY LINKED TO CYSTEINE 69 BY A THIOESTER BOND. TURN KABSCH AND SANDER ALGORITHM CHECKED BY HAND ON THE GRAPHICS DISPLAY.
Has protein modificationY
Nonpolymer details4-HYDROXYCINNAMYL CHROMOPHORE, O(C6H4)CH=CH(C=O), IS COVALENTLY LINKED TO CYSTEINE 69 BY A ...4-HYDROXYCINNAMYL CHROMOPHORE, O(C6H4)CH=CH(C=O), IS COVALENTLY LINKED TO CYSTEINE 69 BY A THIOESTER BOND. SPECTROSCOPICALLY, THE CHROMOPHORE APPEARS TO BE NEGATIVELY CHARGED IN THE CONTEXT OF THE FOLDED PROTEIN IN THE DARK STATE. DURING REFINEMENT, CYS 69 AND THE COVALENTLY BOUND CHROMOPHORE WERE TREATED TOGETHER AS ONE RESIDUE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35.17 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop / Details: used as seeds
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

DetectorDate: Nov 1, 1991
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.4 Å / Num. obs: 19756 / % possible obs: 92.7 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.04
Reflection
*PLUS
Lowest resolution: 9999 Å / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 1.5 Å / Num. unique obs: 3449 / Num. measured obs: 4910 / Rmerge(I) obs: 0.207

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENdata reduction
X-PLOR3.1phasing
RefinementResolution: 1.4→20 Å / σ(F): 3
RfactorNum. reflection% reflection
Rfree0.226 -10 %
Rwork0.186 --
obs0.186 16794 81.4 %
Displacement parametersBiso mean: 13.2 Å2
Refinement stepCycle: LAST / Resolution: 1.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1011 0 11 92 1114
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.57
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.39
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
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.39
LS refinement shell
*PLUS
Highest resolution: 1.4 Å / Lowest resolution: 1.5 Å / Rfactor Rfree: 0.222 / Num. reflection obs: 2030 / Rfactor obs: 0.212

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