5CJE | pdb_00005cje

Structure of CYP107L2

• PDB DOI: https://doi.org/10.2210/pdb5CJE/pdb

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


• Deposited: 2015-07-14 Released: 2016-07-20 
• Deposition Author(s): Pham, T.-V., Han, S.-H., Kim, J.-H., Kim, D.-H., Kang, L.-W.
• Funding Organization(s): National Research Foundation of Korea, Cooperative Research Program for Agriculture Science & Technology Development

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.255 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

Structure of CYP107L2

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

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: 43.89 kDa 
• Atom Count: 3,134 
• Modeled Residue Count: 390 
• Deposited Residue Count: 393 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450 hydroxylase	A	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.255 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.184	α = 90
b = 50.585	β = 98.91
c = 74.638	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHASER	phasing
Coot	model building
DENZO	data processing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-07-20 
Deposition Author(s): Pham, T.-V., Han, S.-H., Kim, J.-H., Kim, D.-H., Kang, L.-W.

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Funding Organization	Location	Grant Number
National Research Foundation of Korea	Korea, Republic Of	2011-0016509
Cooperative Research Program for Agriculture Science & Technology Development	Korea, Republic Of	PJ01127901

Revision History  

• Version 1.0: 2016-07-20
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description