4HJX | pdb_00004hjx

Crystal structure of F2YRS complexed with F2Y

PDB DOI: https://doi.org/10.2210/pdb4HJX/pdb

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

Deposited: 2012-10-14 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: 2.91 Å
R-Value Free:
0.268 (Depositor), 0.273 (DCC)
R-Value Work:
0.211 (Depositor), 0.218 (DCC)
R-Value Observed:
0.213 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 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: 72.54 kDa
Atom Count: 4,977
Modeled Residue Count: 612
Deposited Residue Count: 628
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, 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
F2Y Query on F2Y Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	3,5-difluoro-L-tyrosine C₉ H₉ F₂ N O₃ KPKMCRFCNWVLDA-ZETCQYMHSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.91 Å
R-Value Free: 0.268 (Depositor), 0.273 (DCC)
R-Value Work: 0.211 (Depositor), 0.218 (DCC)
R-Value Observed: 0.213 (Depositor)

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.307	α = 90
b = 101.307	β = 90
c = 71.779	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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Ligand Structure Quality Assessment

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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: 2018-03-14
Changes: Database references
Version 1.3: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2023-12-06
Changes: Data collection