5U93

Structure of the Regulatory Domain of the AraC Family Transcriptional Activator RhaR

PDB DOI: https://doi.org/10.2210/pdb5U93/pdb

Classification: TRANSCRIPTION
Organism(s): Bacteria Latreille et al. 1825
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-12-15 Released: 2017-12-20
Deposition Author(s): Zhao, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.203
R-Value Work: 0.171
R-Value Observed: 0.172

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of the Regulatory Domain of the AraC Family Transcriptional Activator RhaR

Lin, J., Zhao, H., Shaath, D., Wehmeye, G., Kolin, A., Egan, S.

To be published.

Macromolecule Content

Total Structure Weight: 40.24 kDa
Atom Count: 2,812
Modelled Residue Count: 321
Deposited Residue Count: 344
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HTH-type transcriptional activator RhaR	A, B	172	Bacteria Latreille et al. 1825	Mutation(s): 0
UniProt
Find proteins for P09378 (Escherichia coli (strain K12)) Explore P09378 Go to UniProtKB: P09378
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P09378
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RM4 Query on RM4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	beta-L-rhamnopyranose C₆ H₁₂ O₅ SHZGCJCMOBCMKK-YJRYQGEOSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.203
R-Value Work: 0.171
R-Value Observed: 0.172
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.793	α = 90
b = 100.793	β = 90
c = 95.696	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-12-20

Deposition Author(s):

Zhao, H.

Revision History (Full details and data files)

Version 1.0: 2017-12-20
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.2: 2024-11-06
Changes: Data collection, Database references, Structure summary

Prepare Data

Validate Data

Deposit Data

Help and Resources

5U93

Structure of the Regulatory Domain of the AraC Family Transcriptional Activator RhaR

Structure of the Regulatory Domain of the AraC Family Transcriptional Activator RhaR

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)