4RK1 | pdb_00004rk1

Crystal structure of LacI family transcriptional regulator from Enterococcus faecium, Target EFI-512930, with bound ribose

PDB DOI: https://doi.org/10.2210/pdb4RK1/pdb

Classification: TRANSCRIPTION REGULATOR
Organism(s): Enterococcus faecium DO
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-10-11 Released: 2014-10-29
Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Al Obaidi, N., Chamala, S., Attonito, J.D., Scott Glenn, A., Chowdhury, S., Lafleur, J., Siedel, R.D., Hillerich, B., Love, J., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.192 (Depositor), 0.204 (DCC)
R-Value Work:
0.159 (Depositor), 0.174 (DCC)
R-Value Observed:
0.160 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Crystal Structure of LacI Transcriptional Regulator Rbsr from Enterococcus faecium, Target EFI-512930

Patskovsky, Y., Toro, R., Bhosle, R., Al Obaidi, N., Chamala, S., Scott Glenn, A., Attonito, J.D., Chowdhury, S., Lafleur, J., Siedel, R.D., Hillerich, B., Love, J., Whalen, K.L., Gerlt, J.A., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 191.78 kDa
Atom Count: 14,067
Modeled Residue Count: 1,608
Deposited Residue Count: 1,680
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribose transcriptional regulator	A, B, C, D, E A, B, C, D, E, F	280	Enterococcus faecium DO	Mutation(s): 0 Gene Names: rbsR, HMPREF0351_10453
UniProt
Find proteins for I3TZ89 (Enterococcus faecium (strain ATCC BAA-472 / TX0016 / DO)) Explore I3TZ89 Go to UniProtKB: I3TZ89
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I3TZ89
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RIB Query on RIB Download Ideal Coordinates CCD File SDF format, chain DA [auth F] SDF format, chain W [auth D] SDF format, chain Q [auth C] SDF format, chain K [auth B] SDF format, chain G [auth A] SDF format, chain BA [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain W [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] MOL2 format, chain BA [auth E] mmCIF format, chain DA [auth F] mmCIF format, chain W [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A] mmCIF format, chain BA [auth E]	BA [auth E] DA [auth F] G [auth A] K [auth B] Q [auth C] BA [auth E], DA [auth F], G [auth A], K [auth B], Q [auth C], W [auth D]	alpha-D-ribofuranose C₅ H₁₀ O₅ HMFHBZSHGGEWLO-AIHAYLRMSA-N		Interactions Focus chain BA [auth E] Focus chain DA [auth F] Focus chain G [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain W [auth D] Interactions & Density Focus chain BA [auth E] Focus chain DA [auth F] Focus chain G [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain W [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain Y [auth D] SDF format, chain X [auth D] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain GA [auth F] SDF format, chain FA [auth F] SDF format, chain EA [auth F] SDF format, chain CA [auth E] SDF format, chain AA [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain X [auth D] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth F] MOL2 format, chain FA [auth F] MOL2 format, chain EA [auth F] MOL2 format, chain CA [auth E] MOL2 format, chain AA [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain X [auth D] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth F] mmCIF format, chain FA [auth F] mmCIF format, chain EA [auth F] mmCIF format, chain CA [auth E] mmCIF format, chain AA [auth D]	AA [auth D] CA [auth E] EA [auth F] FA [auth F] GA [auth F] AA [auth D], CA [auth E], EA [auth F], FA [auth F], GA [auth F], H [auth A], I [auth A], J [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], R [auth C], S [auth C], T [auth C], U [auth C], V [auth C], X [auth D], Y [auth D], Z [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth D] Focus chain CA [auth E] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain CA [auth E] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.192 (Depositor), 0.204 (DCC)
R-Value Work: 0.159 (Depositor), 0.174 (DCC)
R-Value Observed: 0.160 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.371	α = 90
b = 95.243	β = 119.47
c = 123.602	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-10-29

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2014-10-29
Type: Initial release
Version 1.1: 2015-02-18
Changes: Structure summary
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2024-11-06
Changes: Data collection, Database references, Structure summary