7CUP | pdb_00007cup

Structure of 2,5-dihydroxypridine Dioxygenase from Pseudomonas putida KT2440

PDB DOI: https://doi.org/10.2210/pdb7CUP/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pseudomonas putida KT2440
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-08-23 Released: 2020-12-16
Deposition Author(s): Liu, G.Q., Tang, H.Z.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.213 (Depositor), 0.221 (DCC)
R-Value Work:
0.171 (Depositor), 0.182 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7CUP

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

Literature

2,5-dihydroxypridine Dioxygenase in complex with 2,5-dihydroxypridine and product N-formylmaleamic acid

Liu, G.Q., Tang, H.Z.

(2020) Nat Commun

Macromolecule Content

Total Structure Weight: 243.87 kDa
Atom Count: 17,845
Modeled Residue Count: 2,086
Deposited Residue Count: 2,178
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2,5-dihydroxypyridine 5,6-dioxygenase	A, B, C, D, E A, B, C, D, E, F	363	Pseudomonas putida KT2440	Mutation(s): 0 Gene Names: nicX, PP_3945 EC: 1.13.11.9
UniProt
Find proteins for Q88FY1 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)) Explore Q88FY1 Go to UniProtKB: Q88FY1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q88FY1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE (Subject of Investigation/LOI) Query on FE Download:Ideal Coordinates CCD File SDF format, chain L [auth F] SDF format, chain K [auth E] SDF format, chain J [auth D] SDF format, chain I [auth C] SDF format, chain H [auth B] SDF format, chain G [auth A] MOL2 format, chain L [auth F] MOL2 format, chain K [auth E] MOL2 format, chain J [auth D] MOL2 format, chain I [auth C] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] mmCIF format, chain L [auth F] mmCIF format, chain K [auth E] mmCIF format, chain J [auth D] mmCIF format, chain I [auth C] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A]	G [auth A] H [auth B] I [auth C] J [auth D] K [auth E] G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D] Focus chain K [auth E] Focus chain L [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain J [auth D] Focus chain K [auth E] Focus chain L [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.213 (Depositor), 0.221 (DCC)
R-Value Work: 0.171 (Depositor), 0.182 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.961	α = 90
b = 143.75	β = 90
c = 118.69	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-12-16

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	--

Revision History (Full details and data files)

Version 1.0: 2020-12-16
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Database references, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.