4MM0 | pdb_00004mm0

Crystal Structure Analysis of the Putative Thioether Synthase SgvP Involved in the Tailoring Step of Griseoviridin

• PDB DOI: https://doi.org/10.2210/pdb4MM0/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptomyces griseoviridis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-09-07 Released: 2014-09-17 
• Deposition Author(s): Zhang, H., Huang, L., Yi, M., Cai, T., Zhang, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.214 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Structural Analysis of SgvP: a Putative Thioether Synthase Involved in the Tailoring Step of Griseoviridin

Zhang, H., Huang, L., Yi, M., Cai, T., Zhang, H.

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: 89.04 kDa 
• Atom Count: 6,560 
• Modeled Residue Count: 786 
• Deposited Residue Count: 798 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
P450-like monooxygenase	A, B	399	Streptomyces griseoviridis	Mutation(s): 0  EC: 1.14.13
UniProt
Find proteins for R9USI6 (Streptomyces griseoviridis) Explore R9USI6  Go to UniProtKB:  R9USI6

Small Molecules

Ligands 1 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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.214 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 184.05	α = 90
b = 184.05	β = 90
c = 80.32	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-17 
Deposition Author(s): Zhang, H., Huang, L., Yi, M., Cai, T., Zhang, H.

Revision History  

• Version 1.0: 2014-09-17
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description