7CKI | pdb_00007cki

Crystal structure of Tryptophanyl-tRNA synthetase from Bacillus stearothermophilus in complex with chuangxinmycin and ATP

PDB DOI: https://doi.org/10.2210/pdb7CKI/pdb

Classification: ANTIBIOTIC
Organism(s): Geobacillus stearothermophilus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2020-07-17 Released: 2021-07-21
Deposition Author(s): Lyu, G., Fan, S., Jin, Y., Liu, J., Zou, S., Wu, G., Yang, Z.
Funding Organization(s): National Natural Science Foundation of China (NSFC), Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.208 (Depositor), 0.209 (DCC)
R-Value Work:
0.165 (Depositor), 0.166 (DCC)
R-Value Observed:
0.169 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of Tryptophanyl-tRNA synthetase from Bacillus stearothermophilus in complex with chuangxinmycin and ATP

Lyu, G., Fan, S., Jin, Y., Li, D., Liu, J., Zou, S., Wu, G., Yang, Z.

To be published.

Macromolecule Content

Total Structure Weight: 38.35 kDa
Atom Count: 2,800
Modeled Residue Count: 326
Deposited Residue Count: 330
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophan--tRNA ligase	A	330	Geobacillus stearothermophilus	Mutation(s): 1 Gene Names: trpS EC: 6.1.1.2
UniProt
Find proteins for P00953 (Geobacillus stearothermophilus) Explore P00953 Go to UniProtKB: P00953
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00953
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
9E0 (Subject of Investigation/LOI) Query on 9E0 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(5~{S},6~{R})-5-methyl-7-thia-2-azatricyclo[6.3.1.0^{4,12}]dodeca-1(12),3,8,10-tetraene-6-carboxylic acid C₁₂ H₁₁ N O₂ S DKHFLDXCKWDVMF-UPONEAKYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
K (Subject of Investigation/LOI) Query on K Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	D [auth A], F [auth A], G [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain D [auth A] Focus chain F [auth A] Focus chain G [auth A]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.208 (Depositor), 0.209 (DCC)
R-Value Work: 0.165 (Depositor), 0.166 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.988	α = 90
b = 61.988	β = 90
c = 218.066	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-07-21

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81761128016
National Natural Science Foundation of China (NSFC)	China	81621064
Ministry of Science and Technology (MoST, China)	China	2018YFA0901800