4HK4 | pdb_00004hk4

Crystal structure of apo Tyrosine-tRNA ligase mutant protein

PDB DOI: https://doi.org/10.2210/pdb4HK4/pdb

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

Deposited: 2012-10-15 Released: 2013-04-17
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: 2.30 Å
R-Value Free:
0.277 (Depositor), 0.269 (DCC)
R-Value Work:
0.229 (Depositor), 0.228 (DCC)
R-Value Observed:
0.231 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of apo Tyrosine-tRNA ligase mutant protein

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: 35.85 kDa
Atom Count: 2,492
Modeled Residue Count: 309
Deposited Residue Count: 312
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	312	Methanocaldococcus jannaschii	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
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.277 (Depositor), 0.269 (DCC)
R-Value Work: 0.229 (Depositor), 0.228 (DCC)
R-Value Observed: 0.231 (Depositor)

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.695	α = 90
b = 38.886	β = 90.98
c = 83.061	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-04-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-04-17
Type: Initial release
Version 1.1: 2013-07-10
Changes: Structure summary
Version 1.2: 2015-05-27
Changes: Structure summary
Version 1.3: 2017-11-15
Changes: Refinement description
Version 1.4: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description