7F36 | pdb_00007f36

TacT complexed with acetyl-glycyl-tRNAGly

PDB DOI: https://doi.org/10.2210/pdb7F36/pdb
NAKB: 7F36

Classification: TRANSFERASE
Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2, Escherichia coli
Expression System: Escherichia coli BL21(DE3), Escherichia coli
Mutation(s): Yes

Deposited: 2021-06-15 Released: 2021-12-22
Deposition Author(s): Yashiro, Y., Tomita, K.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Ministry of Education, Culture, Sports, Science and Technology (Japan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free:
0.263 (Depositor), 0.260 (DCC)
R-Value Work:
0.208 (Depositor), 0.210 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Molecular basis of glycyl-tRNAGly acetylation by TacT from Salmonella Typhimurium

Yashiro, Y., Zhang, C., Sakaguchi, Y., Suzuki, T., Tomita, K.

(2021) Cell Rep 37: 110130

DOI: https://doi.org/10.1016/j.celrep.2021.110130

Macromolecule Content

Total Structure Weight: 174.94 kDa
Atom Count: 11,302
Modeled Residue Count: 931
Deposited Residue Count: 980
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acetyltransferase domain-containing protein	A, B, D, E [auth C]	169	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 1 Gene Names: STM3651 EC: 2.3.1
UniProt
Find proteins for Q8ZL98 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZL98 Go to UniProtKB: Q8ZL98
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8ZL98
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (76-MER)	C [auth F], F [auth G], G [auth H], H [auth E]	76	Escherichia coli
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AAC Query on AAC Download Ideal Coordinates CCD File SDF format, chain NA [auth E] MOL2 format, chain NA [auth E] mmCIF format, chain NA [auth E]	NA [auth E]	ACETYLAMINO-ACETIC ACID C₄ H₇ N O₃ OKJIRPAQVSHGFK-UHFFFAOYSA-N		Interactions Focus chain NA [auth E] Interactions & Density Focus chain NA [auth E]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain Z [auth G] SDF format, chain Y [auth C] SDF format, chain XA [auth E] SDF format, chain X [auth D] SDF format, chain WA [auth E] SDF format, chain W [auth F] SDF format, chain VA [auth E] SDF format, chain V [auth F] SDF format, chain UA [auth E] SDF format, chain U [auth F] SDF format, chain TA [auth E] SDF format, chain T [auth F] SDF format, chain SA [auth E] SDF format, chain S [auth F] SDF format, chain RA [auth E] SDF format, chain R [auth F] SDF format, chain QA [auth E] SDF format, chain Q [auth F] SDF format, chain PA [auth E] SDF format, chain P [auth F] SDF format, chain OA [auth E] SDF format, chain O [auth F] SDF format, chain N [auth F] SDF format, chain MA [auth H] SDF format, chain M [auth F] SDF format, chain LA [auth H] SDF format, chain L [auth F] SDF format, chain KA [auth H] SDF format, chain K [auth F] SDF format, chain JA [auth H] SDF format, chain J [auth B] SDF format, chain IA [auth H] SDF format, chain I [auth A] SDF format, chain HA [auth H] SDF format, chain GA [auth H] SDF format, chain FA [auth H] SDF format, chain EA [auth G] SDF format, chain DA [auth G] SDF format, chain CA [auth G] SDF format, chain BA [auth G] SDF format, chain AA [auth G] MOL2 format, chain Z [auth G] MOL2 format, chain Y [auth C] MOL2 format, chain XA [auth E] MOL2 format, chain X [auth D] MOL2 format, chain WA [auth E] MOL2 format, chain W [auth F] MOL2 format, chain VA [auth E] MOL2 format, chain V [auth F] MOL2 format, chain UA [auth E] MOL2 format, chain U [auth F] MOL2 format, chain TA [auth E] MOL2 format, chain T [auth F] MOL2 format, chain SA [auth E] MOL2 format, chain S [auth F] MOL2 format, chain RA [auth E] MOL2 format, chain R [auth F] MOL2 format, chain QA [auth E] MOL2 format, chain Q [auth F] MOL2 format, chain PA [auth E] MOL2 format, chain P [auth F] MOL2 format, chain OA [auth E] MOL2 format, chain O [auth F] MOL2 format, chain N [auth F] MOL2 format, chain MA [auth H] MOL2 format, chain M [auth F] MOL2 format, chain LA [auth H] MOL2 format, chain L [auth F] MOL2 format, chain KA [auth H] MOL2 format, chain K [auth F] MOL2 format, chain JA [auth H] MOL2 format, chain J [auth B] MOL2 format, chain IA [auth H] MOL2 format, chain I [auth A] MOL2 format, chain HA [auth H] MOL2 format, chain GA [auth H] MOL2 format, chain FA [auth H] MOL2 format, chain EA [auth G] MOL2 format, chain DA [auth G] MOL2 format, chain CA [auth G] MOL2 format, chain BA [auth G] MOL2 format, chain AA [auth G] mmCIF format, chain Z [auth G] mmCIF format, chain Y [auth C] mmCIF format, chain XA [auth E] mmCIF format, chain X [auth D] mmCIF format, chain WA [auth E] mmCIF format, chain W [auth F] mmCIF format, chain VA [auth E] mmCIF format, chain V [auth F] mmCIF format, chain UA [auth E] mmCIF format, chain U [auth F] mmCIF format, chain TA [auth E] mmCIF format, chain T [auth F] mmCIF format, chain SA [auth E] mmCIF format, chain S [auth F] mmCIF format, chain RA [auth E] mmCIF format, chain R [auth F] mmCIF format, chain QA [auth E] mmCIF format, chain Q [auth F] mmCIF format, chain PA [auth E] mmCIF format, chain P [auth F] mmCIF format, chain OA [auth E] mmCIF format, chain O [auth F] mmCIF format, chain N [auth F] mmCIF format, chain MA [auth H] mmCIF format, chain M [auth F] mmCIF format, chain LA [auth H] mmCIF format, chain L [auth F] mmCIF format, chain KA [auth H] mmCIF format, chain K [auth F] mmCIF format, chain JA [auth H] mmCIF format, chain J [auth B] mmCIF format, chain IA [auth H] mmCIF format, chain I [auth A] mmCIF format, chain HA [auth H] mmCIF format, chain GA [auth H] mmCIF format, chain FA [auth H] mmCIF format, chain EA [auth G] mmCIF format, chain DA [auth G] mmCIF format, chain CA [auth G] mmCIF format, chain BA [auth G] mmCIF format, chain AA [auth G]	AA [auth G] BA [auth G] CA [auth G] DA [auth G] EA [auth G] AA [auth G], BA [auth G], CA [auth G], DA [auth G], EA [auth G], FA [auth H], GA [auth H], HA [auth H], I [auth A], IA [auth H], J [auth B], JA [auth H], K [auth F], KA [auth H], L [auth F], LA [auth H], M [auth F], MA [auth H], N [auth F], O [auth F], OA [auth E], P [auth F], PA [auth E], Q [auth F], QA [auth E], R [auth F], RA [auth E], S [auth F], SA [auth E], T [auth F], TA [auth E], U [auth F], UA [auth E], V [auth F], VA [auth E], W [auth F], WA [auth E], X [auth D], XA [auth E], Y [auth C], Z [auth G]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain BA [auth G] Focus chain CA [auth G] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain FA [auth H] Focus chain GA [auth H] Focus chain HA [auth H] Focus chain I [auth A] Focus chain IA [auth H] Focus chain J [auth B] Focus chain JA [auth H] Focus chain K [auth F] Focus chain KA [auth H] Focus chain L [auth F] Focus chain LA [auth H] Focus chain M [auth F] Focus chain MA [auth H] Focus chain N [auth F] Focus chain O [auth F] Focus chain OA [auth E] Focus chain P [auth F] Focus chain PA [auth E] Focus chain Q [auth F] Focus chain QA [auth E] Focus chain R [auth F] Focus chain RA [auth E] Focus chain S [auth F] Focus chain SA [auth E] Focus chain T [auth F] Focus chain TA [auth E] Focus chain U [auth F] Focus chain UA [auth E] Focus chain V [auth F] Focus chain VA [auth E] Focus chain W [auth F] Focus chain WA [auth E] Focus chain X [auth D] Focus chain XA [auth E] Focus chain Y [auth C] Focus chain Z [auth G] Interactions & Density Focus chain AA [auth G] Focus chain BA [auth G] Focus chain CA [auth G] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain FA [auth H] Focus chain GA [auth H] Focus chain HA [auth H] Focus chain I [auth A] Focus chain IA [auth H] Focus chain J [auth B] Focus chain JA [auth H] Focus chain K [auth F] Focus chain KA [auth H] Focus chain L [auth F] Focus chain LA [auth H] Focus chain M [auth F] Focus chain MA [auth H] Focus chain N [auth F] Focus chain O [auth F] Focus chain OA [auth E] Focus chain P [auth F] Focus chain PA [auth E] Focus chain Q [auth F] Focus chain QA [auth E] Focus chain R [auth F] Focus chain RA [auth E] Focus chain S [auth F] Focus chain SA [auth E] Focus chain T [auth F] Focus chain TA [auth E] Focus chain U [auth F] Focus chain UA [auth E] Focus chain V [auth F] Focus chain VA [auth E] Focus chain W [auth F] Focus chain WA [auth E] Focus chain X [auth D] Focus chain XA [auth E] Focus chain Y [auth C] Focus chain Z [auth G]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.263 (Depositor), 0.260 (DCC)
R-Value Work: 0.208 (Depositor), 0.210 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.743	α = 90
b = 121.873	β = 91.07
c = 127.257	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-12-22

Deposition Author(s):

Yashiro, Y.

Tomita, K.

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	LS136
Japan Society for the Promotion of Science (JSPS)	Japan	18H03980
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	26113002
Japan Society for the Promotion of Science (JSPS)	Japan	19K16069