5UWZ | pdb_00005uwz

Protein 12 with aldehyde deformylating oxygenase activity from Gloeobacter violaceus

PDB DOI: https://doi.org/10.2210/pdb5UWZ/pdb

Classification: LYASE
Organism(s): Gloeobacter violaceus PCC 7421
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-02-21 Released: 2018-02-28
Deposition Author(s): Wilson, D.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free:
0.167 (Depositor), 0.194 (DCC)
R-Value Work:
0.139 (Depositor)
R-Value Observed:
0.140 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Protein 12 with aldehyde deformylating oxygenase activity from Gloeobacter violaceus

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

To be published.

Macromolecule Content

Total Structure Weight: 27.81 kDa
Atom Count: 2,013
Modeled Residue Count: 219
Deposited Residue Count: 243
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldehyde decarbonylase	A	243	Gloeobacter violaceus PCC 7421	Mutation(s): 0 Gene Names: gll3146 EC: 4.1.99.5
UniProt
Find proteins for Q7NGM3 (Gloeobacter violaceus (strain ATCC 29082 / PCC 7421)) Explore Q7NGM3 Go to UniProtKB: Q7NGM3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7NGM3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
STE Query on STE Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	STEARIC ACID C₁₈ H₃₆ O₂ QIQXTHQIDYTFRH-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.167 (Depositor), 0.194 (DCC)
R-Value Work: 0.139 (Depositor)
R-Value Observed: 0.140 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.842	α = 90
b = 95.424	β = 90
c = 39.255	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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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

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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.