7CL9 | pdb_00007cl9

Androstenedione-bound structure of CYP154C2 from Streptomyces avermitilis in an open conformation

• PDB DOI: https://doi.org/10.2210/pdb7CL9/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptomyces avermitilis MA-4680 = NBRC 14893
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-07-20 Released: 2021-07-21 
• Deposition Author(s): Xu, L.H., Fushinobu, S.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Androstenedione-bound structure of CYP154C2 from Streptomyces avermitilis in an open conformation

Xu, L.H., Fushinobu, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 44.11 kDa 
• Atom Count: 3,392 
• Modeled Residue Count: 398 
• Deposited Residue Count: 400 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450 hydroxylase	A	400	Streptomyces avermitilis MA-4680 = NBRC 14893	Mutation(s): 0  Gene Names: cyp19, SAVERM_3882
UniProt
Find proteins for Q82GL5 (Streptomyces avermitilis (strain ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680)) Explore Q82GL5  Go to UniProtKB:  Q82GL5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
ASD	C [auth A]	4-ANDROSTENE-3-17-DIONE C19 H26 O2 AEMFNILZOJDQLW-QAGGRKNESA-N
PEG	D [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.6	α = 90
b = 80.13	β = 90
c = 120.63	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-07-21 
Deposition Author(s): Xu, L.H., Fushinobu, S.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81402810

Revision History  

• Version 1.0: 2021-07-21
  Type: Initial release
  
• Version 2.0: 2023-09-20
  Type: Coordinate replacement
  Reason: Atoms with unrealistic or zero occupancies
  Changes: Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2023-11-29
  Changes: Refinement description