4Z5Q

Crystal structure of the LnmZ cytochrome P450 hydroxylase from the leinamycin biosynthetic pathway of Streptomyces atroolivaceus S-140 at 1.8 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4Z5Q/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptomyces atroolivaceus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-04-02 Released: 2015-08-12 
• Deposition Author(s): Ma, M., Lohman, J., Rudolf, J., Miller, M.D., Cao, H., Osipiuk, J., Joachimiak, A., Phillips Jr., G.N., Shen, B., Midwest Center for Structural Genomics (MCSG), Enzyme Discovery for Natural Product Biosynthesis (NatPro)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.200 
• R-Value Work: 0.159 
• R-Value Observed: 0.161 

Starting Model: experimental

Literature

Crystal structure of the LnmZ cytochrome P450 hydroxylase from the leinamycin biosynthetic pathway of Streptomyces atroolivaceus S-140

Ma, M., Lohman, J., Rudolf, J., Miller, M.D., Cao, H., Osipiuk, J., Joachimiak, A., Phillips Jr., G.N., Shen, B.

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: 48.51 kDa 
• Atom Count: 3,226 
• Modelled Residue Count: 364 
• Deposited Residue Count: 423 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450 hydroxylase	A	423	Streptomyces atroolivaceus	Mutation(s): 0  Gene Names: LnmZ
UniProt
Find proteins for Q8GGM6 (Streptomyces atroolivaceus) Explore Q8GGM6  Go to UniProtKB:  Q8GGM6

Small Molecules

Ligands 5 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
P33	H [auth A]	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL C14 H30 O8 XPJRQAIZZQMSCM-UHFFFAOYSA-N
1PE	I [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
CL	F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	C [auth A], D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.200 
• R-Value Work: 0.159 
• R-Value Observed: 0.161 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/m34z5q

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.307	α = 90
b = 83.434	β = 97.67
c = 48.192	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-08-12 
Deposition Author(s): Ma, M., Lohman, J., Rudolf, J., Miller, M.D., Cao, H., Osipiuk, J., Joachimiak, A., Phillips Jr., G.N., Shen, B., Midwest Center for Structural Genomics (MCSG), Enzyme Discovery for Natural Product Biosynthesis (NatPro)

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U01GM098248
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01CA106150

Revision History  

• Version 1.0: 2015-08-12
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Derived calculations, Refinement description
• Version 1.2: 2019-12-04
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary