4Z5P

Crystal structure of the LnmA cytochrome P450 hydroxylase from the leinamycin biosynthetic pathway of Streptomyces atroolivaceus S-140 at 1.9 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4Z5P/pdb

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


• Deposited: 2015-04-02 Released: 2015-07-29 
• Deposition Author(s): Ma, M., Lohman, J., Rudolf, J., Miller, M.D., Cao, H., Osipiuk, J., Babnigg, G., Phillips Jr., G.N., Joachimiak, A., 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.217 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the LnmA 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., Babnigg, G., Phillips Jr., G.N., Joachimiak, A., Shen, B.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 90.15 kDa 
• Atom Count: 6,581 
• Modelled Residue Count: 776 
• Deposited Residue Count: 800 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450 hydroxylase	A, B	400	Streptomyces atroolivaceus	Mutation(s): 0  Gene Names: LnmA
UniProt
Find proteins for Q8GGQ1 (Streptomyces atroolivaceus) Explore Q8GGQ1  Go to UniProtKB:  Q8GGQ1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], D [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
PGE	E [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.217 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34z5p

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.759	α = 90
b = 75.454	β = 98.91
c = 93.858	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
XDS	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-07-29 
Deposition Author(s): Ma, M., Lohman, J., Rudolf, J., Miller, M.D., Cao, H., Osipiuk, J., Babnigg, G., Phillips Jr., G.N., Joachimiak, A., Shen, B., Midwest Center for Structural Genomics (MCSG), Enzyme Discovery for Natural Product Biosynthesis (NatPro)

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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: 2015-07-29
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Derived calculations, Refinement description, Source and taxonomy
• 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