4EPZ

Crystal structure of a transcription anti-terminator antagonist UpxZ (BACUNI_04315) from Bacteroides uniformis ATCC 8492 at 1.68 A resolution

PDB DOI: https://doi.org/10.2210/pdb4EPZ/pdb

Classification: TRANSCRIPTION
Organism(s): Bacteroides uniformis ATCC 8492
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-04-17 Released: 2012-07-11
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.68 Å
R-Value Free: 0.196
R-Value Work: 0.168
R-Value Observed: 0.170

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a transcription anti-terminator antagonist UpxZ (BACUNI_04315) from Bacteroides uniformis ATCC 8492 at 1.68 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 19.41 kDa
Atom Count: 1,649
Modelled Residue Count: 154
Deposited Residue Count: 162
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
transcription anti-terminator antagonist UpxZ	A	162	Bacteroides uniformis ATCC 8492	Mutation(s): 0 Gene Names: BACUNI_04315
UniProt
Find proteins for A7V9P0 (Bacteroides uniformis (strain ATCC 8492 / DSM 6597 / CCUG 4942 / CIP 103695 / JCM 5828 / KCTC 5204 / NCTC 13054 / VPI 0061)) Explore A7V9P0 Go to UniProtKB: A7V9P0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A7V9P0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A]	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.68 Å
R-Value Free: 0.196
R-Value Work: 0.168
R-Value Observed: 0.170
Space Group: C 2 2 2₁
Diffraction Data: https://doi.org/10.18430/M34EPZ

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.253	α = 90
b = 81.11	β = 90
c = 105.702	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
BUSTER-TNT	refinement
XDS	data reduction
SHELXD	phasing
BUSTER	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-07-11

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2012-07-11
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2018-01-24
Changes: Database references
Version 1.3: 2023-02-01
Changes: Database references, Derived calculations

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.