8KCZ | pdb_00008kcz

Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1 in complex with 1,4-androstadiene-3,17- dione

PDB DOI: https://doi.org/10.2210/pdb8KCZ/pdb

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

Deposited: 2023-08-08 Released: 2023-08-30
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: 2.30 Å
R-Value Free:
0.223 (Depositor), 0.230 (DCC)
R-Value Work:
0.192 (Depositor), 0.200 (DCC)
R-Value Observed:
0.193 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1 in complex with 1,4-androstadiene-3,17- dione

Song, S.K., Su, Z.D.

To be published.

Macromolecule Content

Total Structure Weight: 55.72 kDa
Atom Count: 3,920
Modeled Residue Count: 523
Deposited Residue Count: 523
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% 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]
ANB (Subject of Investigation/LOI) Query on ANB 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]	ANDROSTA-1,4-DIENE-3,17-DIONE C₁₉ H₂₄ O₂ LUJVUUWNAPIQQI-QAGGRKNESA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.223 (Depositor), 0.230 (DCC)
R-Value Work: 0.192 (Depositor), 0.200 (DCC)
R-Value Observed: 0.193 (Depositor)

Space Group: P 3₁ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.89	α = 90
b = 118.89	β = 90
c = 118.61	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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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-08-30

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-08-30
Type: Initial release

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.