6L2I | pdb_00006l2i

IlvC, a ketol-acid reductoisomerase, from Streptococcus pneumoniae_WT

PDB DOI: https://doi.org/10.2210/pdb6L2I/pdb

Classification: ISOMERASE
Organism(s): Streptococcus pneumoniae D39
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-10-04 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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free:
0.209 (Depositor), 0.210 (DCC)
R-Value Work:
0.194 (Depositor), 0.190 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 77.27 kDa
Atom Count: 5,871
Modelled Residue Count: 647
Deposited Residue Count: 680
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ketol-acid reductoisomerase (NADP(+))	A, B	340	Streptococcus pneumoniae D39	Mutation(s): 0 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q04M32
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP (Subject of Investigation/LOI) Query on NAP Download Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
SO4 (Subject of Investigation/LOI) Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], T [auth B], U [auth B], V [auth B], W [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B]	C [auth A] D [auth A] E [auth A] O [auth B] P [auth B] C [auth A], D [auth A], E [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B]	M [auth B], N [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain M [auth B] Focus chain N [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free: 0.209 (Depositor), 0.210 (DCC)
R-Value Work: 0.194 (Depositor), 0.190 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.063	α = 90
b = 104.349	β = 90
c = 110.942	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-08-12

Deposition Author(s):

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 (Full details and data files)

Version 1.0: 2020-08-12
Type: Initial release
Version 1.1: 2023-11-22
Changes: Advisory, Data collection, Database references, Refinement description
Version 1.2: 2024-10-09
Changes: Structure summary