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- PDB-3phy: PHOTOACTIVE YELLOW PROTEIN, DARK STATE (UNBLEACHED), SOLUTION STR... -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 3phy
TitlePHOTOACTIVE YELLOW PROTEIN, DARK STATE (UNBLEACHED), SOLUTION STRUCTURE, NMR, 26 STRUCTURES
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)
MethodSOLUTION NMR / distance geometry
AuthorsDux, P. / Rubinstenn, G. / Vuister, G.W. / Boelens, R. / Mulder, F.A.A. / Hard, K. / Hoff, W.D. / Kroon, A. / Crielaard, W. / Hellingwerf, K.J. / Kaptein, R.
Citation
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. / Hard, K. / Hoff, W.D. / Kroon, A.R. / Crielaard, W. / Hellingwerf, K.J. / Kaptein, R.
#1: Journal: Biochemistry / Year: 1994
Title: Thiol Ester-Linked P-Coumaric Acid as a New Photoactive Prosthetic Group in a Protein with Rhodopsin-Like Photochemistry
Authors: Hoff, W.D. / Dux, P. / Hard, K. / Devreese, B. / Nugteren-Roodzant, I.M. / Crielaard, W. / Boelens, R. / Kaptein, R. / Van Beeumen, J. / Hellingwerf, K.J.
History
DepositionFeb 6, 1998Processing site: BNL
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)26 / 40LOW ENERGY
Representative

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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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131COSY
141HSQC-NOESY
151HSQC-TOCSY
161HNHA
171HNHB

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Sample preparation

Sample conditionspH: 5.8 / Temperature: 311 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMX600BrukerAMX6005001
Varian AMX500VarianAMX5006002
Varian UNITY PLUS500VarianUNITY PLUS5007503
Varian UNITY PLUS750VarianUNITY PLUS7507504

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: distance geometry / Software ordinal: 1
Details: TWO CONSTRAINT REFINEMENT STEPS OF 0.47 AND 0.58 PS, RESPECTIVELY, WITH AN INITIAL TEMPERATURE OF 2000K, EXCLUDING ELECTROSTATIC INTERACTIONS, WERE DONE.
NMR ensembleConformer selection criteria: LOW ENERGY / Conformers calculated total number: 40 / Conformers submitted total number: 26

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