5UXI | pdb_00005uxi

Protein 4 with aldehyde deformylating oxygenase activity from Nostoc puntiforme

PDB DOI: https://doi.org/10.2210/pdb5UXI/pdb

Classification: LYASE
Organism(s): Nostoc punctiforme PCC 73102
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: 2.00 Å
R-Value Free:
0.268 (Depositor), 0.267 (DCC)
R-Value Work:
0.205 (Depositor), 0.212 (DCC)
R-Value Observed:
0.206 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

Protein 4 with aldehyde deformylating oxygenase activity from Nostoc puntiforme

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

To be published.

Macromolecule Content

Total Structure Weight: 27.09 kDa
Atom Count: 1,918
Modeled Residue Count: 220
Deposited Residue Count: 234
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldehyde decarbonylase	A	234	Nostoc punctiforme PCC 73102	Mutation(s): 0 Gene Names: Npun_R1711 EC: 4.1.99.5
UniProt
Find proteins for B2J1M1 (Nostoc punctiforme (strain ATCC 29133 / PCC 73102)) Explore B2J1M1 Go to UniProtKB: B2J1M1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B2J1M1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DDQ Query on DDQ Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A], D [auth A]	DECYLAMINE-N,N-DIMETHYL-N-OXIDE C₁₂ H₂₇ N O ZRKZFNZPJKEWPC-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.268 (Depositor), 0.267 (DCC)
R-Value Work: 0.205 (Depositor), 0.212 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.655	α = 90
b = 79.655	β = 90
c = 133.055	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	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

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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.