4ZXW | pdb_00004zxw

Crystal structure of SgcC5 protein from Streptomyces globisporus (complex with (R)-(-)-1-(2-naphthyl)-1,2-ethanediol and sucrose)

• PDB DOI: https://doi.org/10.2210/pdb4ZXW/pdb

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


• Deposited: 2015-05-20 Released: 2015-06-17 
• Deposition Author(s): Michalska, K., Bigelow, L., Jedrzejczak, R., Babnigg, G., Lohman, J., Ma, M., Rudolf, J., Chang, C.-Y., Shen, B., Joachimiak, A., 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 
  0.208 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of SgcC5 protein from Streptomyces globisporus

Michalska, K., Bigelow, L., Jedrzejczak, R., Babnigg, G., Lohman, J., Ma, M., Rudolf, J., Chang, C.-Y., Shen, B., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Enzyme Discovery for Natural Product Biosynthesis (NatPro)

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 103.33 kDa 
• Atom Count: 7,291 
• Modeled Residue Count: 886 
• Deposited Residue Count: 924 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C-domain type II peptide synthetase	A, B	462	Streptomyces globisporus	Mutation(s): 0
UniProt
Find proteins for Q8GMG2 (Streptomyces globisporus) Explore Q8GMG2  Go to UniProtKB:  Q8GMG2

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	C, D	2		N/A
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CXS	L [auth B]	3-CYCLOHEXYL-1-PROPYLSULFONIC ACID C9 H19 N O3 S PJWWRFATQTVXHA-UHFFFAOYSA-N
4T7	E [auth A], I [auth B]	(1R)-1-(naphthalen-2-yl)ethane-1,2-diol C12 H12 O2 QFNOPZNUHSDHKZ-LBPRGKRZSA-N
SO4	F [auth A], G [auth A], H [auth A], J [auth B], K [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003	C, D	sucrose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free:  0.208 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34ZXW

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.397	α = 90
b = 105.304	β = 90
c = 108.167	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-06-17 
Deposition Author(s): Michalska, K., Bigelow, L., Jedrzejczak, R., Babnigg, G., Lohman, J., Ma, M., Rudolf, J., Chang, C.-Y., Shen, B., Joachimiak, A., 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	GM094585
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM098248

Revision History  

• Version 1.0: 2015-06-17
  Type: Initial release
  
• Version 1.1: 2016-09-21
  Changes: Source and taxonomy
• Version 1.2: 2017-09-06
  Changes: Author supporting evidence, Derived calculations
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-09-27
  Changes: Data collection, Database references, Refinement description, Structure summary