8JOJ | pdb_00008joj

Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1 in complex with 9,11-epoxy-17-hydroxypregn-4-ene-3,20-dione actate

PDB DOI: https://doi.org/10.2210/pdb8JOJ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Rhodococcus erythropolis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-06-07 Released: 2023-07-12
Deposition Author(s): Hu, Y.L., Li, X., Cheng, X.Y., Song, S.K., Su, Z.D.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.82 Å
R-Value Free:
0.234 (Depositor), 0.235 (DCC)
R-Value Work:
0.189 (Depositor), 0.189 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1 in complex with 9,11-epoxy-17-hydroxypregn-4-ene-3,20-dione actate

Song, S.K., Hu, Y.L., Li, X., Su, Z.D.

To be published.

Macromolecule Content

Total Structure Weight: 55.85 kDa
Atom Count: 3,925
Modeled Residue Count: 523
Deposited Residue Count: 523
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-ketosteroid dehydrogenase	A	523	Rhodococcus erythropolis	Mutation(s): 0 Gene Names: kstD1, BS297_24040, rerp_49010, RERY_47440 EC: 1.3.99.4
UniProt
Find proteins for Q9RA02 (Rhodococcus erythropolis) Explore Q9RA02 Go to UniProtKB: Q9RA02
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9RA02
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
UU0 (Subject of Investigation/LOI) Query on UU0 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	9,11-epoxy-17-hydroxypregn-4-ene-3,20-dione actate C₂₄ H₃₂ O₆ FOTDGVYUEIORAP-ITJRCREZSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.82 Å
R-Value Free: 0.234 (Depositor), 0.235 (DCC)
R-Value Work: 0.189 (Depositor), 0.189 (DCC)

Space Group: P 3₁ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.603	α = 90
b = 119.603	β = 90
c = 117.304	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-07-12

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-07-12
Type: Initial release
Version 1.1: 2024-05-29
Changes: Data collection

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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.