3MAE | pdb_00003mae

CRYSTAL STRUCTURE OF PROBABLE DIHYDROLIPOAMIDE ACETYLTRANSFERASE FROM LISTERIA MONOCYTOGENES 4b F2365

PDB DOI: https://doi.org/10.2210/pdb3MAE/pdb

Classification: TRANSFERASE
Organism(s): Listeria monocytogenes serotype 4b str. F2365
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-03-23 Released: 2010-04-07
Deposition Author(s): Patskovsky, Y., Toro, R., Gilmore, M., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.234 (Depositor), 0.232 (DCC)
R-Value Work:
0.192 (Depositor), 0.193 (DCC)
R-Value Observed:
0.193 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

CRYSTAL STRUCTURE OF A CATALYTIC DOMAIN OF DIHYDROLIPOAMIDE ACETYLTRANSFERASE FROM LISTERIA MONOCYTOGENES 4b F2365

Patskovsky, Y., Toro, R., Gilmore, M., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 86.19 kDa
Atom Count: 5,666
Modeled Residue Count: 713
Deposited Residue Count: 768
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-oxoisovalerate dehydrogenase E2 component, dihydrolipoamide acetyltransferase	A, B, C	256	Listeria monocytogenes serotype 4b str. F2365	Mutation(s): 0 Gene Names: LMOf2365_1391 EC: 2.3.1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain Y [auth C] SDF format, chain X [auth C] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain BA [auth C] SDF format, chain AA [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain X [auth C] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain BA [auth C] MOL2 format, chain AA [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain X [auth C] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain BA [auth C] mmCIF format, chain AA [auth C]	AA [auth C] BA [auth C] E [auth A] F [auth A] G [auth A] AA [auth C], BA [auth C], E [auth A], F [auth A], G [auth A], H [auth A], Q [auth B], R [auth B], X [auth C], Y [auth C], Z [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain O [auth A] SDF format, chain M [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain DA [auth C] SDF format, chain CA [auth C] MOL2 format, chain S [auth B] MOL2 format, chain O [auth A] MOL2 format, chain M [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain DA [auth C] MOL2 format, chain CA [auth C] mmCIF format, chain S [auth B] mmCIF format, chain O [auth A] mmCIF format, chain M [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain DA [auth C] mmCIF format, chain CA [auth C]	CA [auth C] DA [auth C] I [auth A] J [auth A] K [auth A] CA [auth C], DA [auth C], I [auth A], J [auth A], K [auth A], M [auth A], O [auth A], S [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain O [auth A] Focus chain S [auth B] Interactions & Density Focus chain CA [auth C] Focus chain DA [auth C] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain O [auth A] Focus chain S [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain W [auth C] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain P [auth B] SDF format, chain N [auth A] SDF format, chain L [auth A] SDF format, chain EA [auth C] SDF format, chain D [auth A] MOL2 format, chain W [auth C] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain P [auth B] MOL2 format, chain N [auth A] MOL2 format, chain L [auth A] MOL2 format, chain EA [auth C] MOL2 format, chain D [auth A] mmCIF format, chain W [auth C] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain P [auth B] mmCIF format, chain N [auth A] mmCIF format, chain L [auth A] mmCIF format, chain EA [auth C] mmCIF format, chain D [auth A]	D [auth A] EA [auth C] L [auth A] N [auth A] P [auth B] D [auth A], EA [auth C], L [auth A], N [auth A], P [auth B], T [auth B], U [auth B], V [auth B], W [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain EA [auth C] Focus chain L [auth A] Focus chain N [auth A] Focus chain P [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth C] Interactions & Density Focus chain D [auth A] Focus chain EA [auth C] Focus chain L [auth A] Focus chain N [auth A] Focus chain P [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.234 (Depositor), 0.232 (DCC)
R-Value Work: 0.192 (Depositor), 0.193 (DCC)
R-Value Observed: 0.193 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.221	α = 90
b = 173.008	β = 90
c = 131.061	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-04-07

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2010-04-07
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2018-11-21
Changes: Data collection, Structure summary
Version 1.3: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2024-02-21
Changes: Data collection, Database references