9BQ4 | pdb_00009bq4

YTP-E E148D, a weakly yellow thermostable protein

PDB DOI: https://doi.org/10.2210/pdb9BQ4/pdb

Classification: FLUORESCENT PROTEIN
Organism(s): synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-05-09 Released: 2024-09-04
Deposition Author(s): Padgett, C., Ogbeifun, V., DeVore, N.M.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.281 (Depositor), 0.285 (DCC)
R-Value Work:
0.221 (Depositor), 0.234 (DCC)
R-Value Observed:
0.227 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9BQ4

This is version 3.0 of the entry. See complete history.

Literature

The Crystal Structure of Thermal Green Protein Q66E (TGP-E) and Yellow Thermostable Protein (YTP-E) E148D

Anderson, M.R., Padgett, C.M., Ogbeifun, V.O., DeVore, N.M.

(2024) SynBio 2: 298-310

DOI: https://doi.org/10.3390/synbio2030018

Macromolecule Content

Total Structure Weight: 113.06 kDa
Atom Count: 6,913
Modeled Residue Count: 848
Deposited Residue Count: 996
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Weakly yellow thermostable protein YTP-E	A, B, C, D	249	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CRU Query on CRU	A, B, C, D	L-PEPTIDE LINKING	C₁₆ H₁₅ N₃ O₆		GLU, TYR, GLY

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.281 (Depositor), 0.285 (DCC)
R-Value Work: 0.221 (Depositor), 0.234 (DCC)
R-Value Observed: 0.227 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.784	α = 90
b = 137.777	β = 97.7
c = 74.556	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
CrysalisPro	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-09-04

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	2117129

Revision History (Full details and data files)

Version 1.0: 2024-09-04
Type: Initial release
Version 2.0: 2024-09-25
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
Version 2.1: 2024-11-13
Changes: Database references, Structure summary
Version 3.0: 2026-03-18
Changes: Polymer sequence

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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.