2ZP1 | pdb_00002zp1

Structual basis of iodo-tyrosine recognition by engineered archeal tyrosyl-tRNA synthetase

PDB DOI: https://doi.org/10.2210/pdb2ZP1/pdb

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

Deposited: 2008-06-22 Released: 2009-02-17
Deposition Author(s): Oki, K., Kobayashi, T., Sakamoto, K., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.220 (Depositor), 0.220 (DCC)
R-Value Work:
0.193 (Depositor), 0.192 (DCC)
R-Value Observed:
0.193 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Structual Basis of Iodo-Tyrosine Recognition by Engineered Archeal Tyrosyl-tRNA Synthetase

Oki, K., Kobayashi, T., Sakamoto, K., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 36.42 kDa
Atom Count: 2,768
Modeled Residue Count: 308
Deposited Residue Count: 314
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosyl-tRNA synthetase	A	314	Methanocaldococcus jannaschii	Mutation(s): 4 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
IYR Query on IYR 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-IODO-TYROSINE C₉ H₁₀ I N O₃ UQTZMGFTRHFAAM-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: 1.70 Å
R-Value Free: 0.220 (Depositor), 0.220 (DCC)
R-Value Work: 0.193 (Depositor), 0.192 (DCC)
R-Value Observed: 0.193 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.201	α = 90
b = 102.201	β = 90
c = 71.904	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-02-17

Deposition Author(s):

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2009-02-17
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-11-10
Changes: Database references, Derived calculations
Version 1.3: 2023-11-01
Changes: Data collection, Refinement description

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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.