4HPW | pdb_00004hpw

Crystal structure of Tyrosine-tRNA ligase mutant complexed with unnatural amino acid 3-o-methyl-Tyrosine

PDB DOI: https://doi.org/10.2210/pdb4HPW/pdb

Classification: LIGASE
Organism(s): Methanocaldococcus jannaschii DSM 2661
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2012-10-24 Released: 2013-10-30
Deposition Author(s): Yu, Y., Zhou, Q., Dong, J., Li, J., Xiaoxuan, L., Mukherjee, A., Ouyang, H., Nilges, M., Li, H., Gao, F., Gong, W., Lu, Y., Wang, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.251 (Depositor), 0.245 (DCC)
R-Value Work:
0.197 (Depositor), 0.193 (DCC)
R-Value Observed:
0.200 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of Tyrosine-tRNA ligase mutant complexed with unnatural amino acid 3-o-methyl-Tyrosine

Yu, Y., Zhou, Q., Dong, J., Li, J., Xiaoxuan, L., Mukherjee, A., Ouyang, H., Nilges, M., Li, H., Gao, F., Gong, W., Lu, Y., Wang, J.

To be published.

Macromolecule Content

Total Structure Weight: 35.51 kDa
Atom Count: 2,586
Modeled Residue Count: 310
Deposited Residue Count: 310
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine--tRNA ligase	A	310	Methanocaldococcus jannaschii DSM 2661	Mutation(s): 6 Gene Names: tyrS, MJ0389 EC: 6.1.1.1
UniProt
Find proteins for Q57834 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q57834 Go to UniProtKB: Q57834
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q57834
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3YM Query on 3YM 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]	3-methoxy-L-tyrosine C₁₀ H₁₃ N O₄ PFDUUKDQEHURQC-ZETCQYMHSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.251 (Depositor), 0.245 (DCC)
R-Value Work: 0.197 (Depositor), 0.193 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.629	α = 90
b = 38.83	β = 90.75
c = 82.957	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-10-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-10-30
Type: Initial release
Version 1.1: 2015-05-27
Changes: Structure summary
Version 1.2: 2019-07-17
Changes: Data collection, Refinement description
Version 1.3: 2024-02-28
Changes: Data collection, Database references, Derived calculations