5YZX | pdb_00005yzx

Crystal structure of E.coli LysU T146D mutant

PDB DOI: https://doi.org/10.2210/pdb5YZX/pdb

Classification: LIGASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2017-12-16 Released: 2018-12-19
Deposition Author(s): Fang, P., Guo, M.
Funding Organization(s): National Institutes of Health, Shanghai Pujiang Program, National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.269 (Depositor), 0.269 (DCC)
R-Value Work:
0.236 (Depositor), 0.237 (DCC)
R-Value Observed:
0.238 (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

A proposed role for MSC to reserve the canonical function in high eukaryotes prior to stimuli

Zheng, L., Ali, H., Wang, J., Guo, M., Fang, P.

To be published.

Macromolecule Content

Total Structure Weight: 183.12 kDa
Atom Count: 11,574
Modeled Residue Count: 1,453
Deposited Residue Count: 1,575
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysine--tRNA ligase, heat inducible	A, B, C	525	Escherichia coli K-12	Mutation(s): 1 Gene Names: lysU, b4129, JW4090 EC: 6.1.1.6
UniProt
Find proteins for P0A8N5 (Escherichia coli (strain K12)) Explore P0A8N5 Go to UniProtKB: P0A8N5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A8N5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B4P Query on B4P Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain L [auth C] SDF format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain L [auth C] MOL2 format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain L [auth C] mmCIF format, chain D [auth A]	D [auth A], H [auth B], L [auth C]	BIS(ADENOSINE)-5'-TETRAPHOSPHATE C₂₀ H₂₈ N₁₀ O₁₉ P₄ YOAHKNVSNCMZGQ-XPWFQUROSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Focus chain L [auth C] Interactions & Density Focus chain D [auth A] Focus chain H [auth B] Focus chain L [auth C]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain O [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C]	E [auth A] F [auth A] G [auth A] I [auth B] J [auth B] E [auth A], F [auth A], G [auth A], I [auth B], J [auth B], K [auth B], M [auth C], N [auth C], O [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.269 (Depositor), 0.269 (DCC)
R-Value Work: 0.236 (Depositor), 0.237 (DCC)
R-Value Observed: 0.238 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.544	α = 90
b = 249.855	β = 90
c = 179.652	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-12-19

Deposition Author(s):

Fang, P.

Guo, M.

Funding Organization	Location	Grant Number
National Institutes of Health	United States	GM100136
National Institutes of Health	United States	GM106134
Shanghai Pujiang Program	China	17PJ1410800
National Natural Science Foundation of China	China	21778067
National Natural Science Foundation of China	China	21778064

Revision History (Full details and data files)

Version 1.0: 2018-12-19
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description

5YZX | pdb_00005yzx

Crystal structure of E.coli LysU T146D mutant

Literature

A proposed role for MSC to reserve the canonical function in high eukaryotes prior to stimuli

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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