8E02 | pdb_00008e02

Crystal structure of photoactive yellow protein (PYP); F96oCNF T103V construct

PDB DOI: https://doi.org/10.2210/pdb8E02/pdb

Classification: SIGNALING PROTEIN
Organism(s): Halorhodospira halophila
Expression System: Escherichia coli str. K-12 substr. DH10B
Mutation(s): Yes

Deposited: 2022-08-08 Released: 2022-08-24
Deposition Author(s): Kirsh, J.M., Weaver, J.B., Boxer, S.G.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.09 Å
R-Value Free:
0.169 (Depositor), 0.169 (DCC)
R-Value Work:
0.138 (Depositor), 0.140 (DCC)
R-Value Observed:
0.139 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Protic and Aprotic Interactions Systematically Perturbed and Mapped via MD and IR Spectroscopy

Kirsh, J.M., Kozuch, J., Weaver, J.B., Boxer, S.G.

To be published.

Macromolecule Content

Total Structure Weight: 14.08 kDa
Atom Count: 1,235
Modeled Residue Count: 125
Deposited Residue Count: 125
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photoactive yellow protein	A	125	Halorhodospira halophila	Mutation(s): 1 Gene Names: pyp
UniProt
Find proteins for P16113 (Halorhodospira halophila) Explore P16113 Go to UniProtKB: P16113
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P16113
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HC4 Query on HC4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	4'-HYDROXYCINNAMIC ACID C₉ H₈ O₃ NGSWKAQJJWESNS-ZZXKWVIFSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.09 Å
R-Value Free: 0.169 (Depositor), 0.169 (DCC)
R-Value Work: 0.138 (Depositor), 0.140 (DCC)
R-Value Observed: 0.139 (Depositor)

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.305	α = 90
b = 66.305	β = 90
c = 40.692	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-08-24

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	2R35GM11804406
National Science Foundation (NSF, United States)	United States	1915727

Revision History (Full details and data files)

Version 1.0: 2022-08-24
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description
Version 1.2: 2023-11-15
Changes: Data collection, Derived calculations

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.