4XR9 | pdb_00004xr9

Crystal structure of CalS8 from Micromonospora echinospora cocrystallized with NAD and TDP-glucose

• PDB DOI: https://doi.org/10.2210/pdb4XR9/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Micromonospora echinospora
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-01-20 Released: 2015-02-11 
• Deposition Author(s): Michalska, K., Bigelow, L., Endres, M., Babnigg, G., Bingman, C.A., Yennamalli, R.M., Singh, S., Kharel, M.K., Thorson, J.S., Phillips Jr., G.N., 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: 1.95 Å
• R-Value Free: 
  0.205 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of CalS8 from Micromonospora echinospora

Michalska, K., Bigelow, L., Endres, M., Babnigg, G., Bingman, C.A., Yennamalli, R.M., Singh, S., Kharel, M.K., Thorson, J.S., Phillips Jr., G.N., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 96.62 kDa 
• Atom Count: 7,091 
• Modeled Residue Count: 909 
• Deposited Residue Count: 912 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CalS8	A, B	456	Micromonospora echinospora	Mutation(s): 1  Gene Names: calS8
UniProt
Find proteins for Q8KNF6 (Micromonospora echinospora) Explore Q8KNF6  Go to UniProtKB:  Q8KNF6

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	C [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
TMP	E [auth A]	THYMIDINE-5'-PHOSPHATE C10 H15 N2 O8 P GYOZYWVXFNDGLU-XLPZGREQSA-N
GOL	F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.205 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.682	α = 90
b = 87.04	β = 103.59
c = 70.66	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-02-11 
Deposition Author(s): Michalska, K., Bigelow, L., Endres, M., Babnigg, G., Bingman, C.A., Yennamalli, R.M., Singh, S., Kharel, M.K., Thorson, J.S., Phillips Jr., G.N., 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: 2015-02-11
  Type: Initial release
  
• Version 1.1: 2015-08-19
  Changes: Other
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description