2D01	Signaling Protein	date	Jul 21, 2005
title	Wild Type Photoactive Yellow Protein, P65 Form
authors	N.Shimizu, H.Kamikubo, Y.Yamazaki, Y.Imamoto, M.Kataoka
compound		source
Molecule: Photoactive Yellow Protein Chain: A Synonym: Photoreceptor, Pyp Engineered: Yes		Organism_scientific: Halorhodospira Halophila Organism_taxid: 1053 Gene: Pyp Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21de3 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet
symmetry	Space Group: P 65	R_factor 0.152 R_Free 0.189
crystal cell	length a length b length c angle alpha angle beta angle gamma 40.422 40.422 118.131 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	1.34 Å
ligand	HC4	enzyme
note	2D01 (Molecule of the Month:pdb183)
Gene Ontology	Chain Function Process Component A
Primary reference	The Crystal Structure of the R52Q Mutant Demonstrates a Role for R52 in Chromophore pK(a) Regulation in Photoactive Yellow Protein(,)., Shimizu N, Kamikubo H, Yamazaki Y, Imamoto Y, Kataoka M, Biochemistry. 2006 Mar 21;45(11):3542-7. PMID:16533035

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (54 Kb) [Save to disk] Biological Unit Coordinates (2d01.pdb1.gz) 50 Kb LPC: Ligand-Protein Contacts for 2D01 CSU: Contacts of Structural Units for 2D01 Likely Quarternary Molecular Structure file(s) for 2D01 Structure Factors (159 Kb) Retrieve 2D01 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2D01 from S2C, [Save to disk] Re-refined 2d01 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2D01 in 3D

Proteopedia, because life has more than 2D. On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure. On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Visual 3D analysis of 2D01

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 2D01, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2d01_A] [2d01] SWISS-PROT database: [P16113] Domain organization of [PYP_HALHA] by SWISSPFAM Domain found in 2D01: [PAS ] by SMART

Other resources with information on 2D01

Community annotation for 2D01 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

You may enter another PDB ID code

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]

---

OCA© by Jaime Prilusky, 1996-2014,2022 Bioinformatics Unit Weizmann Institute of Science

---