4N44 | pdb_00004n44

Crystal structure of oxidized form of thiolase from Clostridium acetobutylicum

PDB DOI: https://doi.org/10.2210/pdb4N44/pdb

Classification: TRANSFERASE
Organism(s): Clostridium acetobutylicum EA 2018
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-10-08 Released: 2014-10-08
Deposition Author(s): Kim, S., Ha, S.C., Ahn, J.W., Kim, E.J., Lim, J.H., Kim, K.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free:
0.208 (Depositor), 0.222 (DCC)
R-Value Work:
0.168 (Depositor), 0.183 (DCC)
R-Value Observed:
0.170 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structural insight into redox-switch regulatory mechanism of thiolase from the n-butanol synthesizing bacterium, Clostridium acetobutylicum

Kim, S., Ha, S.C., Ahn, J.W., Kim, E.J., Lim, J.H., Son, H.C., Ryu, Y.S., Lee, S.K., Kim, K.J.

To be published.

Macromolecule Content

Total Structure Weight: 85.14 kDa
Atom Count: 6,249
Modeled Residue Count: 784
Deposited Residue Count: 800
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl-CoA acetyltransferase	A, B	400	Clostridium acetobutylicum EA 2018	Mutation(s): 0 Gene Names: CEA_G2880 EC: 2.3.1.9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B]	G [auth B], H [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain G [auth B] Focus chain H [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth B], F [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free: 0.208 (Depositor), 0.222 (DCC)
R-Value Work: 0.168 (Depositor), 0.183 (DCC)
R-Value Observed: 0.170 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 203.227	α = 90
b = 53.987	β = 90
c = 72.968	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-10-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-10-08
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-10-09
Changes: Structure summary