6L2Z | pdb_00006l2z

IlvC, a ketol-acid reductoisomerase, from Streptococcus pnuemoniae_D191G

• PDB DOI: https://doi.org/10.2210/pdb6L2Z/pdb

• Classification: ISOMERASE
• Organism(s): Streptococcus pneumoniae D39
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2019-10-07 Released: 2020-08-12 
• Deposition Author(s): Gyuhee, K., Donghyuk, S., Sumin, L., Jaesook, Y., Sangho, L.
• Funding Organization(s): Rural Development Administration, National Research Foundation (Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 
  0.244 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of IlvC, a Ketol-Acid Reductoisomerase, from Streptococcus Pneumoniae.

Kim, G.H., Shin, D.H., Lee, S.M., Yoon, J.S., Lee, S.H.

(2019) Crystals (Basel) 9

• DOI: https://doi.org/10.3390/cryst9110551

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: 76.55 kDa 
• Atom Count: 5,688 
• Modeled Residue Count: 648 
• Deposited Residue Count: 680 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ketol-acid reductoisomerase (NADP(+))	A, B	340	Streptococcus pneumoniae D39	Mutation(s): 1  Gene Names: ilvC, SPD_0406 EC: 1.1.1.86
UniProt
Find proteins for Q04M32 (Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466)) Explore Q04M32  Go to UniProtKB:  Q04M32

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP (Subject of Investigation/LOI)	C [auth A], G [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
SO4 (Subject of Investigation/LOI)	D [auth A], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL (Subject of Investigation/LOI)	E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NH4 (Subject of Investigation/LOI)	I [auth B]	AMMONIUM ION H4 N QGZKDVFQNNGYKY-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free:  0.244 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.88	α = 90
b = 104.511	β = 90
c = 112.478	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
Coot	model building
REFMAC	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-08-12 
Deposition Author(s): Gyuhee, K., Donghyuk, S., Sumin, L., Jaesook, Y., Sangho, L.

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Funding Organization	Location	Grant Number
Rural Development Administration	Korea, Republic Of	PJ01367602
National Research Foundation (Korea)	Korea, Republic Of	NRF-2018R1A2B6004367
National Research Foundation (Korea)	Korea, Republic Of	NRF-2019R1A6A7076041
National Research Foundation (Korea)	Korea, Republic Of	SRC-2017R1A5A1014560

Revision History  

• Version 1.0: 2020-08-12
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary