6O3F | pdb_00006o3f

Crystal Structure of Lysyl-tRNA Synthetase from Chlamydia trachomatis with complexed with L-lysine and a difluoro cyclohexyl chromone ligand

PDB DOI: https://doi.org/10.2210/pdb6O3F/pdb

Classification: LIGASE
Organism(s): Chlamydia trachomatis L2b/UCH-1/proctitis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-02-26 Released: 2019-03-27
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.205 (Depositor), 0.207 (DCC)
R-Value Work:
0.163 (Depositor), 0.166 (DCC)
R-Value Observed:
0.164 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of Lysyl-tRNA Synthetase from Chlamydia trachomatis with complexed with L-lysine and a difluoro cyclohexyl chromone ligand

Dranow, D.M., Abendroth, J., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 125.16 kDa
Atom Count: 8,795
Modeled Residue Count: 1,034
Deposited Residue Count: 1,058
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine--tRNA ligase	A, B	529	Chlamydia trachomatis L2b/UCH-1/proctitis	Mutation(s): 0 Gene Names: lysS, CTLon_0150 EC: 6.1.1.6
UniProt
Find proteins for B0BAN6 (Chlamydia trachomatis serovar L2b (strain UCH-1/proctitis)) Explore B0BAN6 Go to UniProtKB: B0BAN6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B0BAN6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FYB Query on FYB Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain X [auth B] MOL2 format, chain C [auth A] MOL2 format, chain X [auth B] mmCIF format, chain C [auth A] mmCIF format, chain X [auth B]	C [auth A], X [auth B]	~{N}-[[4,4-bis(fluoranyl)-1-oxidanyl-cyclohexyl]methyl]-6-fluoranyl-4-oxidanylidene-chromene-2-carboxamide C₁₇ H₁₆ F₃ N O₄ PJBRCGHQNUWERQ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain X [auth B] Interactions & Density Focus chain C [auth A] Focus chain X [auth B]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain KA [auth B] MOL2 format, chain KA [auth B] mmCIF format, chain KA [auth B]	KA [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain KA [auth B] Interactions & Density Focus chain KA [auth B]
LYS Query on LYS Download:Ideal Coordinates CCD File SDF format, chain V [auth A] SDF format, chain TA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain TA [auth B] mmCIF format, chain V [auth A] mmCIF format, chain TA [auth B]	TA [auth B], V [auth A]	LYSINE C₆ H₁₅ N₂ O₂ KDXKERNSBIXSRK-YFKPBYRVSA-O		Interactions Focus chain TA [auth B] Focus chain V [auth A] Interactions & Density Focus chain TA [auth B] Focus chain V [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain NA [auth B] SDF format, chain O [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain O [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain O [auth A]	NA [auth B], O [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain NA [auth B] Focus chain O [auth A] Interactions & Density Focus chain NA [auth B] Focus chain O [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain L [auth A] SDF format, chain LA [auth B] SDF format, chain Q [auth A] SDF format, chain S [auth A] SDF format, chain M [auth A] SDF format, chain HA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain S [auth A] MOL2 format, chain M [auth A] MOL2 format, chain HA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain S [auth A] mmCIF format, chain M [auth A] mmCIF format, chain HA [auth B]	EA [auth B] HA [auth B] L [auth A] LA [auth B] M [auth A] EA [auth B], HA [auth B], L [auth A], LA [auth B], M [auth A], Q [auth A], S [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain EA [auth B] Focus chain HA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain Q [auth A] Focus chain S [auth A] Interactions & Density Focus chain EA [auth B] Focus chain HA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain Q [auth A] Focus chain S [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain GA [auth B] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain MA [auth B] SDF format, chain PA [auth B] SDF format, chain R [auth A] SDF format, chain W [auth B] SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain U [auth A] SDF format, chain T [auth A] SDF format, chain SA [auth B] SDF format, chain RA [auth B] SDF format, chain QA [auth B] SDF format, chain P [auth A] SDF format, chain OA [auth B] SDF format, chain N [auth A] SDF format, chain K [auth A] SDF format, chain JA [auth B] SDF format, chain IA [auth B] SDF format, chain FA [auth B] SDF format, chain F [auth A] SDF format, chain D [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain PA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain W [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain U [auth A] MOL2 format, chain T [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain RA [auth B] MOL2 format, chain QA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain D [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain PA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain W [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain U [auth A] mmCIF format, chain T [auth A] mmCIF format, chain SA [auth B] mmCIF format, chain RA [auth B] mmCIF format, chain QA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain D [auth A]	AA [auth B] BA [auth B] CA [auth B] D [auth A] DA [auth B] AA [auth B], BA [auth B], CA [auth B], D [auth A], DA [auth B], E [auth A], F [auth A], FA [auth B], G [auth A], GA [auth B], H [auth A], I [auth A], IA [auth B], J [auth A], JA [auth B], K [auth A], MA [auth B], N [auth A], OA [auth B], P [auth A], PA [auth B], QA [auth B], R [auth A], RA [auth B], SA [auth B], T [auth A], U [auth A], W [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain D [auth A] Focus chain DA [auth B] Focus chain E [auth A] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain T [auth A] Focus chain U [auth A] Focus chain W [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain D [auth A] Focus chain DA [auth B] Focus chain E [auth A] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain T [auth A] Focus chain U [auth A] Focus chain W [auth B] Focus chain Y [auth B] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.205 (Depositor), 0.207 (DCC)
R-Value Work: 0.163 (Depositor), 0.166 (DCC)
R-Value Observed: 0.164 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.49	α = 90
b = 57.28	β = 95.19
c = 138.19	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2019-03-27

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2019-03-27
Type: Initial release
Version 1.1: 2020-03-11
Changes: Data collection
Version 1.2: 2023-10-11
Changes: Data collection, Database references, Refinement description