9JP5 | pdb_00009jp5

Phthalate 3,4-dioxygenase from Rhodococcus jostii RHA1

PDB DOI: https://doi.org/10.2210/pdb9JP5/pdb

Classification: OXIDOREDUCTASE
Organism(s): Rhodococcus jostii RHA1
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: 2.88 Å
R-Value Free:
0.306 (Depositor), 0.306 (DCC)
R-Value Work:
0.247 (Depositor), 0.247 (DCC)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

phthalate 3,4-dioxygenase from Rhodococcus jostii RHA1

Kumar, K.A.

To be published.

Macromolecule Content

Total Structure Weight: 325.26 kDa
Atom Count: 20,893
Modeled Residue Count: 2,526
Deposited Residue Count: 2,860
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phthalate 3,4-dioxygenase alpha subunit	A, C, E, G	507	Rhodococcus jostii RHA1	Mutation(s): 0 Gene Names: padAa, RHA1_ro08167, RHA1_ro10208 EC: 1.14.12
UniProt
Find proteins for Q0RWD5 (Rhodococcus jostii (strain RHA1)) Explore Q0RWD5 Go to UniProtKB: Q0RWD5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q0RWD5
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phthalate 3,4-dioxygenase beta subunit	B, D, F, H	208	Rhodococcus jostii RHA1	Mutation(s): 0 Gene Names: padAb1, padAb, padAb2, RHA1_ro08166, RHA1_ro10209 EC: 1.14.12
UniProt
Find proteins for Q68YB5 (Rhodococcus jostii (strain RHA1)) Explore Q68YB5 Go to UniProtKB: Q68YB5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q68YB5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FES (Subject of Investigation/LOI) Query on FES Download:Ideal Coordinates CCD File SDF format, chain O [auth G] SDF format, chain M [auth E] SDF format, chain K [auth C] SDF format, chain I [auth A] MOL2 format, chain O [auth G] MOL2 format, chain M [auth E] MOL2 format, chain K [auth C] MOL2 format, chain I [auth A] mmCIF format, chain O [auth G] mmCIF format, chain M [auth E] mmCIF format, chain K [auth C] mmCIF format, chain I [auth A]	I [auth A], K [auth C], M [auth E], O [auth G]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain K [auth C] Focus chain M [auth E] Focus chain O [auth G] Interactions & Density Focus chain I [auth A] Focus chain K [auth C] Focus chain M [auth E] Focus chain O [auth G]
FE2 (Subject of Investigation/LOI) Query on FE2 Download:Ideal Coordinates CCD File SDF format, chain P [auth G] SDF format, chain N [auth E] SDF format, chain L [auth C] SDF format, chain J [auth A] MOL2 format, chain P [auth G] MOL2 format, chain N [auth E] MOL2 format, chain L [auth C] MOL2 format, chain J [auth A] mmCIF format, chain P [auth G] mmCIF format, chain N [auth E] mmCIF format, chain L [auth C] mmCIF format, chain J [auth A]	J [auth A], L [auth C], N [auth E], P [auth G]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain L [auth C] Focus chain N [auth E] Focus chain P [auth G] Interactions & Density Focus chain J [auth A] Focus chain L [auth C] Focus chain N [auth E] Focus chain P [auth G]