3IG2

The Crystal Structure of a Putative Phenylalanyl-tRNA synthetase (PheRS) beta chain domain from Bacteroides fragilis to 2.1A

PDB DOI: https://doi.org/10.2210/pdb3IG2/pdb

Classification: LIGASE
Organism(s): Bacteroides fragilis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-07-27 Released: 2009-09-01
Deposition Author(s): Stein, A.J., Sather, A., Hendricks, R., Keigher, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free: 0.236
R-Value Work: 0.195
R-Value Observed: 0.197

wwPDB Validation 3D Report Full Report

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

Literature

The Crystal Structure of a Putative Phenylalanyl-tRNA synthetase (PheRS) beta chain domain from Bacteroides fragilis to 2.1A

Stein, A.J., Sather, A., Hendricks, R., Keigher, L., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 96.87 kDa
Atom Count: 6,285
Modelled Residue Count: 768
Deposited Residue Count: 852
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phenylalanyl-tRNA synthetase beta chain	A, B, C, D	213	Bacteroides fragilis	Mutation(s): 0 Gene Names: BF2565, BF2590, pheT EC: 6.1.1.20
UniProt
Find proteins for Q5LC76 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / NCTC 9343 / Onslow)) Explore Q5LC76 Go to UniProtKB: Q5LC76
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5LC76
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain E [auth C] MOL2 format, chain E [auth C]	E [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth C] Interactions & Density Focus chain E [auth C]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free: 0.236
R-Value Work: 0.195
R-Value Observed: 0.197
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.496	α = 99.04
b = 60.335	β = 100.37
c = 78.805	γ = 105.08

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
SHELX	phasing
MLPHARE	phasing
DM	phasing
ARP/wARP	model building
Coot	model building

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-09-01

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2009-09-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description

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.