5UXG | pdb_00005uxg

Protein 84 with aldehyde deformylating oxygenase activity from Sulfolobus tokodaii (monoclinic)

PDB DOI: https://doi.org/10.2210/pdb5UXG/pdb

Classification: LYASE
Organism(s): Sulfurisphaera tokodaii str. 7
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-02-22 Released: 2018-02-28
Deposition Author(s): Wilson, D.K., Mak, W.S., Siegel, J.B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free:
0.223 (Depositor), 0.229 (DCC)
R-Value Work:
0.195 (Depositor), 0.206 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 5UXG

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

Literature

Protein 84 with aldehyde deformylating oxygenase activity from Sulfolobus tokodaii (monoclinic)

Wilson, D.K., Mak, W.S., Siegel, J.B.

To be published.

Macromolecule Content

Total Structure Weight: 52.12 kDa
Atom Count: 3,741
Modeled Residue Count: 423
Deposited Residue Count: 440
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
aldehyde deformylating oxygenase	A, B	220	Sulfurisphaera tokodaii str. 7	Mutation(s): 0 Gene Names: ST1620, STK_16200
UniProt
Find proteins for Q970H5 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore Q970H5 Go to UniProtKB: Q970H5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q970H5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free: 0.223 (Depositor), 0.229 (DCC)
R-Value Work: 0.195 (Depositor), 0.206 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.536	α = 90
b = 64.849	β = 116.86
c = 71.299	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2018-02-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-02-28
Type: Initial release
Version 1.1: 2024-03-06
Changes: Data collection, Database references
Version 1.2: 2024-04-03
Changes: Refinement description

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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.