9LPC | pdb_00009lpc

Crystal structure of Escherichia coli trptophanyl-tRNA synthetase in complex with tRNA(Trp)

PDB DOI: https://doi.org/10.2210/pdb9LPC/pdb
NAKB: 9LPC

Classification: LIGASE/RNA
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-01-24 Released: 2025-05-07
Deposition Author(s): Peng, X., Chen, B., Zhou, H.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.82 Å
R-Value Free:
0.271 (Depositor), 0.248 (DCC)
R-Value Work:
0.236 (Depositor)
R-Value Observed:
0.238 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9LPC

This is version 1.0 of the entry. See complete history.

Literature

The lineage-specific tRNA recognition mechanism of bacterial trptophanyl-tRNA synthetase and its implications for inhibitor discover

Peng, X., Xia, K., Huang, Q., Xiang, M., Han, L., Qiu, H., Gu, Q., Chen, B., Zhou, H.

To be published.

Macromolecule Content

Total Structure Weight: 125.01 kDa
Atom Count: 7,463
Modeled Residue Count: 782
Deposited Residue Count: 830
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophan--tRNA ligase	A, B	340	Escherichia coli	Mutation(s): 0 Gene Names: trpS, ACU57_16550, B6R15_000448, B6R31_002275, BANRA_02015, BCB93_002501, BGM66_002290, BGZ_04191, BK383_21195, BKL28_001915... trpS, ACU57_16550, B6R15_000448, B6R31_002275, BANRA_02015, BCB93_002501, BGM66_002290, BGZ_04191, BK383_21195, BKL28_001915, BMT91_03555, BvCmsNSP007_00090, BXT93_04920, C0P57_000786, C2R31_002885, C3F40_19370, CG704_07870, CIG67_21025, CTR35_001866, D9D43_04205, DD762_12005, DL968_00250, DNQ45_04190, DTL43_13995, DU321_12325, E4K51_10330, E6D34_04225, EIA08_11870, EPS97_04620, F7F11_12075, F7N46_14665, F9413_17445, F9461_03030, F9B07_12605, FGAF848_25410, FKO60_13960, FOI11_018845, FOI11_04335, FPS11_03390, FZU14_04195, G3V95_06005, G4A38_16925, G4A47_18515, G5603_11025, GAI89_06310, GNW61_08470, GOP25_12480, GP944_08250, GQE86_01825, GQN24_10725, HEP34_002452, HI055_002233, HJQ60_002846, HL563_11055, HL601_09110, HLX92_09755, HLZ50_06610, HMV95_07850, HVW04_17215, HVW43_18350, HVY77_01760, I6H00_19775, IH772_08800, J0541_002134, JNP96_25720, NCTC10764_03793, NCTC10974_00460, NCTC9044_01447, NCTC9073_00479, NCTC9077_00527, NCTC9706_02656, P6223_000209, Q2V20_09290, QDW62_01780, QO046_14075, R8G00_13645, SAMEA3472044_01080, SAMEA3472056_01981, SAMEA3752557_02035 EC: 6.1.1.2
UniProt
Find proteins for E2QFN4 (Escherichia coli) Explore E2QFN4 Go to UniProtKB: E2QFN4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E2QFN4
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism	Image
Entity ID: 2
tRNA(Trp)	C, D	75	Escherichia coli
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.82 Å
R-Value Free: 0.271 (Depositor), 0.248 (DCC)
R-Value Work: 0.236 (Depositor)
R-Value Observed: 0.238 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.788	α = 98.5
b = 63.206	β = 97.25
c = 91.629	γ = 100.04

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data scaling
xia2	data reduction
MERLOT	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-05-07

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22177140

Revision History (Full details and data files)

Version 1.0: 2025-05-07
Type: Initial release

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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.