9JP7 | pdb_00009jp7

4,5-dihydroxyphthalate decarboxylase from Comamonas testosteroni (strain DSM 14576 / KF-1)

PDB DOI: https://doi.org/10.2210/pdb9JP7/pdb

Classification: LYASE
Organism(s): Comamonas testosteroni KF-1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-09-25 Released: 2024-10-30
Deposition Author(s): Kumar, K.A., Kumar, P.
Funding Organization(s): Department of Biotechnology (DBT, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.05 Å
R-Value Free:
0.335 (Depositor), 0.338 (DCC)
R-Value Work:
0.264 (Depositor), 0.265 (DCC)

Starting Model: in silico
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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

4,5-dihydroxyphthalate decarboxylase from Comamonas testosteroni (strain DSM 14576 / KF-1)

Kumar, K.A.

To be published.

Macromolecule Content

Total Structure Weight: 157.83 kDa
Atom Count: 10,450
Modeled Residue Count: 1,289
Deposited Residue Count: 1,396
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4,5-dihydroxyphthalate decarboxylase	A, B, C, D	349	Comamonas testosteroni KF-1	Mutation(s): 0 Gene Names: CtesDRAFT_PD2040 EC: 4.1.1.55
UniProt
Find proteins for B7WQU9 (Comamonas testosteroni (strain DSM 14576 / KF-1)) Explore B7WQU9 Go to UniProtKB: B7WQU9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B7WQU9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain H [auth D] MOL2 format, chain H [auth D] mmCIF format, chain H [auth D]	H [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth D] Interactions & Density Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.05 Å
R-Value Free: 0.335 (Depositor), 0.338 (DCC)
R-Value Work: 0.264 (Depositor), 0.265 (DCC)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.045	α = 90
b = 270.201	β = 90
c = 113.627	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-10-30

Deposition Author(s):

Funding Organization	Location	Grant Number
Department of Biotechnology (DBT, India)	India	DBT-2771-BIO-CNA

Revision History (Full details and data files)

Version 1.0: 2024-10-30
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.