6BLJ | pdb_00006blj

Crystal structure of cytoplasmic Serine-tRNA ligase from Naegleria fowleri in complex with AMP

PDB DOI: https://doi.org/10.2210/pdb6BLJ/pdb

Classification: LIGASE
Organism(s): Naegleria fowleri
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-11-10 Released: 2017-12-20
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.191 (Depositor), 0.195 (DCC)
R-Value Work:
0.158 (Depositor), 0.161 (DCC)
R-Value Observed:
0.159 (Depositor)

Starting Model: experimental
View more details

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 cytoplasmic Serine-tRNA ligase from Neisseria fowlerii in complex with AMP

Abendroth, J., Lorimer, D.D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 167.14 kDa
Atom Count: 11,672
Modeled Residue Count: 1,339
Deposited Residue Count: 1,455
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine-tRNA ligase	A, B, C	485	Naegleria fowleri	Mutation(s): 0 Gene Names: Nfow_scaffold00184

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP Query on AMP Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] SDF format, chain H [auth C] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain H [auth C] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain H [auth C]	D [auth A], F [auth B], H [auth C]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Focus chain H [auth C] Interactions & Density Focus chain D [auth A] Focus chain F [auth B] Focus chain H [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C]	E [auth A], G [auth B], I [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.191 (Depositor), 0.195 (DCC)
R-Value Work: 0.158 (Depositor), 0.161 (DCC)
R-Value Observed: 0.159 (Depositor)

Diffraction Data:

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 168.19	α = 90
b = 168.19	β = 90
c = 111.5	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
MoRDa	phasing
Coot	model building
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2017-12-20

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2017-12-20
Type: Initial release
Version 2.0: 2018-01-10
Changes: Atomic model, Derived calculations
Version 2.1: 2023-10-04
Changes: Data collection, Database references, Refinement description