3D6U | pdb_00003d6u

Crystal structure of 4-(trifluoromethyldiazirinyl)phenylalanyl-tRNA synthetase

PDB DOI: https://doi.org/10.2210/pdb3D6U/pdb
Entry: 3D6U supersedes: 2Q1G

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

Deposited: 2008-05-20 Released: 2008-05-27
Deposition Author(s): Liu, W., Tippmann, E., Mack, A.V., Schultz, P.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.274 (Depositor), 0.273 (DCC)
R-Value Work:
0.201 (Depositor), 0.199 (DCC)
R-Value Observed:
0.204 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

A genetically encoded diazirine photocrosslinker in Escherichia coli

Tippmann, E., Liu, W., Summerer, D., Mack, A.V., Schultz, P.G.

(2007) Chembiochem 8: 2210-2214

PubMed: 18000916 Search on PubMed
DOI: https://doi.org/10.1002/cbic.200700460
Primary Citation Related Structures:
3D6U, 3D6V

Organizational Affiliation

Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd, La Jolla, CA 92037, USA.

Macromolecule Content

Total Structure Weight: 36.45 kDa
Atom Count: 2,618
Modeled Residue Count: 306
Deposited Residue Count: 314
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosyl-tRNA synthetase	A	314	Methanocaldococcus jannaschii	Mutation(s): 7 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
T11 Query on T11 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]	4-[3-(TRIFLUOROMETHYL)DIAZIRIDIN-3-YL]-L-PHENYLALANINE C₁₁ H₁₂ F₃ N₃ O₂ XCRAOXMHVJUSSJ-QMMMGPOBSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
BME Query on BME 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]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-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: 2.20 Å
R-Value Free: 0.274 (Depositor), 0.273 (DCC)
R-Value Work: 0.201 (Depositor), 0.199 (DCC)
R-Value Observed: 0.204 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.779	α = 90
b = 102.779	β = 90
c = 70.78	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-05-27

Deposition Author(s):

This entry supersedes: 2Q1G

Revision History (Full details and data files)

Version 1.0: 2008-05-27
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-10-20
Changes: Database references, Derived calculations

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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.