5VL1 | pdb_00005vl1

Crystal Structure of Lysyl-tRNA Synthetase from Mycobacterium ulcerans complexed with L-lysine

PDB DOI: https://doi.org/10.2210/pdb5VL1/pdb

Classification: LIGASE
Organism(s): Mycobacterium ulcerans Agy99
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-04-24 Released: 2017-05-10
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.204 (Depositor), 0.208 (DCC)
R-Value Work:
0.177 (Depositor), 0.181 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5VL1

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of Lysyl-tRNA Synthetase from Mycobacterium ulcerans complexed with L-lysine

Dranow, D.M., Lorimer, D.D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 227.83 kDa
Atom Count: 15,427
Modeled Residue Count: 1,941
Deposited Residue Count: 2,024
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine--tRNA ligase	A, B, C, D	506	Mycobacterium ulcerans Agy99	Mutation(s): 0 Gene Names: lysS, MUL_4181 EC: 6.1.1.6
UniProt
Find proteins for A0PV47 (Mycobacterium ulcerans (strain Agy99)) Explore A0PV47 Go to UniProtKB: A0PV47
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0PV47
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain L [auth C] SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain N [auth D] MOL2 format, chain L [auth C] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain N [auth D] mmCIF format, chain L [auth C] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A], I [auth B], L [auth C], N [auth D]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain N [auth D]
LYS Query on LYS Download:Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain M [auth C] SDF format, chain J [auth B] SDF format, chain F [auth A] MOL2 format, chain O [auth D] MOL2 format, chain M [auth C] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] mmCIF format, chain O [auth D] mmCIF format, chain M [auth C] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A]	F [auth A], J [auth B], M [auth C], O [auth D]	LYSINE C₆ H₁₅ N₂ O₂ KDXKERNSBIXSRK-YFKPBYRVSA-O		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain O [auth D]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A], K [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.204 (Depositor), 0.208 (DCC)
R-Value Work: 0.177 (Depositor), 0.181 (DCC)
R-Value Observed: 0.178 (Depositor)

Diffraction Data:

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.04	α = 90.38
b = 96.69	β = 104.84
c = 105.56	γ = 117.15

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2017-05-10

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2017-05-10
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.