5CWE | pdb_00005cwe

Structure of CYP107L2 from Streptomyces avermitilis with lauric acid

• PDB DOI: https://doi.org/10.2210/pdb5CWE/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptomyces avermitilis MA-4680 = NBRC 14893
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-07-28 Released: 2016-08-03 
• Deposition Author(s): Pham, T.-V., Han, S.-H., Kim, J.-H., Kim, D.-H., Kang, L.-W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 
  0.301 (Depositor), 0.302 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.229 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: experimental

Literature

Structure of CYP107L2 from Streptomyces avermitilis with lauric acid

Pham, T.-V., Han, S.-H., Kim, J.-H., Kim, D.-H., Kang, L.-W.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 88.28 kDa 
• Atom Count: 6,370 
• Modeled Residue Count: 786 
• Deposited Residue Count: 786 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450 hydroxylase	A, B	393	Streptomyces avermitilis MA-4680 = NBRC 14893	Mutation(s): 0  Gene Names: cyp8, SAV_1987
UniProt
Find proteins for Q82LM3 (Streptomyces avermitilis (strain ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680)) Explore Q82LM3  Go to UniProtKB:  Q82LM3

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	E [auth A], H [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
DAO	D [auth A], G [auth B]	LAURIC ACID C12 H24 O2 POULHZVOKOAJMA-UHFFFAOYSA-N
SO4	C [auth A], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free:  0.301 (Depositor), 0.302 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.229 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.08	α = 90
b = 118.371	β = 105.51
c = 66.039	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data processing
MOLREP	model building
PHASER	phasing
HKL-2000	data processing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-03 
Deposition Author(s): Pham, T.-V., Han, S.-H., Kim, J.-H., Kim, D.-H., Kang, L.-W.

Revision History  

• Version 1.0: 2016-08-03
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description