3IG2 | pdb_00003ig2

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 (Depositor), 0.250 (DCC)
R-Value Work:
0.195 (Depositor), 0.216 (DCC)
R-Value Observed:
0.197 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3IG2

This is version 1.3 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
Modeled Residue Count: 768
Deposited Residue Count: 852
Unique protein chains: 1

Macromolecules

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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 / LMG 10263 / NCTC 9343 / Onslow / VPI 2553 / EN-2)) Explore Q5LC76 Go to UniProtKB: Q5LC76
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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] mmCIF 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 (Depositor), 0.250 (DCC)
R-Value Work: 0.195 (Depositor), 0.216 (DCC)
R-Value Observed: 0.197 (Depositor)

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

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View more in-depth experimental data

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
Version 1.3: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.