4UMZ | pdb_00004umz

PikC D50N mutant in complex with the engineered substrate mimic bearing a 2-dimethylaminomethylbenzoate group

• PDB DOI: https://doi.org/10.2210/pdb4UMZ/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Streptomyces venezuelae
• Expression System: Escherichia coli K-12
• Mutation(s): Yes 


• Deposited: 2014-05-22 Released: 2015-06-17 
• Deposition Author(s): Podust, L.M., Vieira, D.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 
  0.245 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Recognition of Synthetic Substrates by P450 Pikc

Podust, L.M.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 98.68 kDa 
• Atom Count: 6,716 
• Modeled Residue Count: 791 
• Deposited Residue Count: 872 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME P450 HYDROXYLASE PIKC	A, B	436	Streptomyces venezuelae	Mutation(s): 1  EC: 1.14.15.33
UniProt
Find proteins for O87605 (Streptomyces venezuelae) Explore O87605  Go to UniProtKB:  O87605

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], E [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
XJO	D [auth A], F [auth B]	(3R,4S,5S,7R,9E,11R,12R)-12-ethyl-3,5,7,11-tetramethyl-2,8-dioxooxacyclododec-9-en-4-yl 2-[(dimethylamino)methyl]benzoate C27 H39 N O5 MOCRSXQIFXBPAF-JBTKYFGMSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free:  0.245 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.061	α = 90
b = 110.703	β = 90
c = 151.626	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-06-17 
Deposition Author(s): Podust, L.M., Vieira, D.F.

Revision History  

• Version 1.0: 2015-06-17
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description