5DX6 | pdb_00005dx6

Acetolactate Synthase from Klebsiella pneumoniae soaked with beta-fluoropyruvate

PDB DOI: https://doi.org/10.2210/pdb5DX6/pdb

Classification: TRANSFERASE
Organism(s): Klebsiella pneumoniae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-09-23 Released: 2016-09-28
Deposition Author(s): Latta, A.J., McLeish, M.J., Andrews, F.H.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.190 (Depositor), 0.201 (DCC)
R-Value Work:
0.151 (Depositor), 0.161 (DCC)
R-Value Observed:
0.152 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Characterization of Acetolactate Synthase from Klebsiella pneumoniae

Latta, A.J., McLeish, M.J., Andrews, F.H.

To be published.

Macromolecule Content

Total Structure Weight: 126.32 kDa
Atom Count: 9,100
Modeled Residue Count: 1,098
Deposited Residue Count: 1,158
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetolactate synthase, catabolic	A, B	579	Klebsiella pneumoniae	Mutation(s): 0 Gene Names: budB, ilvK EC: 2.2.1.6
UniProt
Find proteins for P27696 (Klebsiella pneumoniae) Explore P27696 Go to UniProtKB: P27696
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P27696
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5GY Query on 5GY Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-[(1R)-2-fluoro-1-hydroxyethyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium C₁₄ H₂₂ F N₄ O₈ P₂ S RCUDZGRKYWDHTO-LLVKDONJSA-O		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
TPP Query on TPP Download:Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	THIAMINE DIPHOSPHATE C₁₂ H₁₉ N₄ O₇ P₂ S AYEKOFBPNLCAJY-UHFFFAOYSA-O		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
65S Query on 65S Download:Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	3-fluoro-2-oxopropanoic acid C₃ H₃ F O₃ CXABZTLXNODUTD-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], G [auth B], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.190 (Depositor), 0.201 (DCC)
R-Value Work: 0.151 (Depositor), 0.161 (DCC)
R-Value Observed: 0.152 (Depositor)

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.8	α = 90
b = 134.01	β = 95.5
c = 110.772	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2016-09-28

Deposition Author(s):

Latta, A.J.

McLeish, M.J.

Andrews, F.H.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	--

Revision History (Full details and data files)

Version 1.0: 2016-09-28
Type: Initial release
Version 1.1: 2017-09-20
Changes: Author supporting evidence, Derived calculations
Version 1.2: 2019-11-27
Changes: Author supporting evidence
Version 1.3: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description