4HJR | pdb_00004hjr

Crystal structure of F2YRS

PDB DOI: https://doi.org/10.2210/pdb4HJR/pdb

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

Deposited: 2012-10-13 Released: 2013-03-13
Deposition Author(s): Wang, J., Tian, C., Gong, W., Li, F., Shi, P., Li, J., Ding, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.298 (Depositor), 0.304 (DCC)
R-Value Work:
0.242 (Depositor), 0.249 (DCC)
R-Value Observed:
0.245 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4HJR

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

Literature

A genetically encoded 19F NMR probe for tyrosine phosphorylation.

Li, F., Shi, P., Li, J., Yang, F., Wang, T., Zhang, W., Gao, F., Ding, W., Li, D., Li, J., Xiong, Y., Sun, J., Gong, W., Tian, C., Wang, J.

(2013) Angew Chem Int Ed Engl 52: 3958-3962

PubMed: 23450644 Search on PubMed
DOI: https://doi.org/10.1002/anie.201300463
Primary Citation Related Structures:
4HJR, 4HJX

Organizational Affiliation

Laboratory of Non-coding RNA, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China.

Macromolecule Content

Total Structure Weight: 72.1 kDa
Atom Count: 5,025
Modeled Residue Count: 615
Deposited Residue Count: 628
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-tRNA ligase	A, B	314	Methanocaldococcus jannaschii DSM 2661	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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.298 (Depositor), 0.304 (DCC)
R-Value Work: 0.242 (Depositor), 0.249 (DCC)
R-Value Observed: 0.245 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.636	α = 90
b = 72.175	β = 91.27
c = 81.744	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-03-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-03-13
Type: Initial release
Version 1.1: 2013-05-22
Changes: Database references
Version 1.2: 2023-09-20
Changes: Data collection, Database references, 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.