4WXE | pdb_00004wxe

CRYSTAL STRUCTURE OF A LACI REGULATOR FROM LACTOBACILLUS CASEI (LSEI_2103, TARGET EFI-512911) WITH BOUND TRIS

PDB DOI: https://doi.org/10.2210/pdb4WXE/pdb

Classification: TRANSCRIPTION
Organism(s): Lacticaseibacillus paracasei ATCC 334
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-11-13 Released: 2014-11-26
Deposition Author(s): Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Wasserman, S.R., Attonito, J.D., Scott Glenn, A., Chamala, S., Chowdhury, S., Lafleur, J., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.168 (Depositor), 0.178 (DCC)
R-Value Work:
0.146 (Depositor), 0.158 (DCC)
R-Value Observed:
0.147 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

CRYSTAL STRUCTURE OF A LACI REGULATOR FROM LACTOBACILLUS CASEI (LSEI_2103, TARGET EFI-512911) WITH BOUND TRIS

Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Wasserman, S.R., Attonito, J.D., Scott Glenn, A., Chamala, S., Chowdhury, S., Lafleur, J., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

To be published.

Macromolecule Content

Total Structure Weight: 33.58 kDa
Atom Count: 2,594
Modeled Residue Count: 278
Deposited Residue Count: 303
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, LacI family	A	303	Lacticaseibacillus paracasei ATCC 334	Mutation(s): 0 Gene Names: LSEI_2103
UniProt
Find proteins for Q036L9 (Lacticaseibacillus paracasei (strain ATCC 334 / BCRC 17002 / CCUG 31169 / CIP 107868 / KCTC 3260 / NRRL B-441)) Explore Q036L9 Go to UniProtKB: Q036L9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q036L9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
MG Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Modified Residues 1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
MSE Query on MSE	A	MET	Selenomethionine	C₅ H₁₁ N O₂ Se

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.168 (Depositor), 0.178 (DCC)
R-Value Work: 0.146 (Depositor), 0.158 (DCC)
R-Value Observed: 0.147 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.047	α = 90
b = 108.047	β = 90
c = 121.477	γ = 120

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-11-26

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2014-11-26
Type: Initial release
Version 1.1: 2015-10-07
Changes: Experimental preparation
Version 1.2: 2024-11-13
Changes: Data collection, Database references, Derived calculations, Structure summary