4ZNM | pdb_00004znm

Crystal structure of SgcC5 protein from Streptomyces globisporus (apo form)

• PDB DOI: https://doi.org/10.2210/pdb4ZNM/pdb

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


• Deposited: 2015-05-04 Released: 2015-05-27 
• 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: 2.00 Å
• R-Value Free: 
  0.192 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Literature

Crystal structure of SgcC5 protein from Streptomyces globisporus (apo form)

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: 102.59 kDa 
• Atom Count: 7,418 
• Modeled Residue Count: 887 
• 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	E [auth A], G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	C [auth A], D [auth A], F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A, B	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.192 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34ZNM

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.596	α = 90
b = 104.542	β = 90
c = 108.465	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-05-27 
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: 2015-05-27
  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: 2017-11-22
  Changes: Refinement description
• Version 1.4: 2019-12-25
  Changes: Author supporting evidence
• Version 1.5: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary