3VKC | pdb_00003vkc

Crystal structure of MoeO5 soaked with pyrophosphate

• PDB DOI: https://doi.org/10.2210/pdb3VKC/pdb

• Classification: TRANSFERASE
• Organism(s): Streptomyces viridosporus ATCC 14672
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-11-12 Released: 2012-05-09 
• Deposition Author(s): Ren, F., Ko, T.-P., Huang, C.-H., Guo, R.-T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 
  0.186 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

Insights into the mechanism of the antibiotic-synthesizing enzyme MoeO5 from crystal structures of different complexes

Ren, F., Ko, T.-P., Feng, X., Huang, C.-H., Chan, H.-C., Hu, Y., Wang, K., Ma, Y., Liang, P.-H., Wang, A.H.-J., Oldfield, E., Guo, R.-T.

(2012) Angew Chem Int Ed Engl 51: 4157-4160

• PubMed: 22431288 
• DOI: https://doi.org/10.1002/anie.201108002
• Primary Citation Related Structures: 
  3VK5, 3VKA, 3VKB, 3VKC, 3VKD

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Organizational Affiliation: 
• Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.

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: 63.17 kDa 
• Atom Count: 4,426 
• Modeled Residue Count: 506 
• Deposited Residue Count: 572 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MoeO5	A, B	286	Streptomyces viridosporus ATCC 14672	Mutation(s): 0  Gene Names: moeO5
UniProt
Find proteins for A0A011 (Streptomyces viridosporus) Explore A0A011  Go to UniProtKB:  A0A011

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FPQ	D [auth A], F [auth B]	(2R)-3-(phosphonooxy)-2-{[(2Z,6E)-3,7,11-trimethyldodeca-2,6,10-trien-1-yl]oxy}propanoic acid C18 H31 O7 P SLQQIKXGDCLCGX-XLGHFPRDSA-N
POP	E [auth B]	PYROPHOSPHATE 2- H2 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-L
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free:  0.186 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.735	α = 66.7
b = 59.721	β = 71.15
c = 59.062	γ = 65.96

Software Package:

Software Name	Purpose
Blu-Ice	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-09 
Deposition Author(s): Ren, F., Ko, T.-P., Huang, C.-H., Guo, R.-T.

Revision History  

• Version 1.0: 2012-05-09
  Type: Initial release
  
• Version 1.1: 2015-04-29
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description