8W40 | pdb_00008w40

Crystal structure of a computationally designed metalloprotein containing the metal-chelating, fluorogenic, non-canonical amino acid 3-(8-hydroxyquinolin-3-yl)-L-alanine: zinc-bound form

PDB DOI: https://doi.org/10.2210/pdb8W40/pdb

Classification: FLUORESCENT PROTEIN, METAL BINDING PROTEIN
Organism(s): Saccharolobus solfataricus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-02-22 Released: 2025-02-26
Deposition Author(s): Kelly, P.I., Henderson, J.H., Mills, J.H.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.164 (Depositor), 0.163 (DCC)
R-Value Work:
0.130 (Depositor), 0.135 (DCC)
R-Value Observed:
0.131 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

Computational design of a fluorogenic metalloprotein containing the non-canonical amino acid 3-(8-hydroxyquinolin-3-yl)-L-alanine

Kelly, P.I., Henderson, J.N., Mills, J.H.

To be published.

Macromolecule Content

Total Structure Weight: 30.25 kDa
Atom Count: 2,377
Modeled Residue Count: 247
Deposited Residue Count: 258
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydroxyquinonline fluorescent protein	A	258	Saccharolobus solfataricus	Mutation(s): 0 EC: 4.1.1.48
UniProt
Find proteins for Q06121 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q06121 Go to UniProtKB: Q06121
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q06121
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A], E [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HQA Query on HQA	A	L-PEPTIDE LINKING	C₁₂ H₁₂ N₂ O₃		ALA

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.164 (Depositor), 0.163 (DCC)
R-Value Work: 0.130 (Depositor), 0.135 (DCC)
R-Value Observed: 0.131 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.593	α = 90
b = 62.593	β = 90
c = 121.416	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-02-26

Deposition Author(s):

Henderson, J.H.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM136996-04

Revision History (Full details and data files)

Version 1.0: 2025-02-26
Type: Initial release

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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.