5A5H | pdb_00005a5h

The crystal structure of the GST-like domains complex of EPRS C92SC105SC123S mutant-AIMP2

PDB DOI: https://doi.org/10.2210/pdb5A5H/pdb

Classification: TRANSLATION
Organism(s): Homo sapiens
Expression System: Escherichia coli B, Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2015-06-18 Released: 2016-06-29
Deposition Author(s): Cho, H.Y., Kang, B.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free:
0.227 (Depositor), 0.239 (DCC)
R-Value Work:
0.172 (Depositor), 0.190 (DCC)
R-Value Observed:
0.174 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

The Crystal Structure of the Gst-Like Domains Complex of Eprs C92Sc105Sc123S Mutant-Aimp2

Cho, H.Y., Kang, B.S.

To be published.

Macromolecule Content

Total Structure Weight: 184.78 kDa
Atom Count: 11,755
Modeled Residue Count: 1,480
Deposited Residue Count: 1,660
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BIFUNCTIONAL GLUTAMATE/PROLINE--TRNA LIGASE	A, C, E, G	175	Homo sapiens	Mutation(s): 3 EC: 6.1.1.15 (PDB Primary Data), 6.1.1.17 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P07814 (Homo sapiens) Explore P07814 Go to UniProtKB: P07814
PHAROS: P07814 GTEx: ENSG00000136628
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07814
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
AMINOACYL TRNA SYNTHASE COMPLEX-INTERACTING MULTIFUNCTIONA L PROTEIN 2	B, D, F, H	240	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q13155 (Homo sapiens) Explore Q13155 Go to UniProtKB: Q13155
PHAROS: Q13155 GTEx: ENSG00000106305
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13155
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, C, E, G	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free: 0.227 (Depositor), 0.239 (DCC)
R-Value Work: 0.172 (Depositor), 0.190 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.687	α = 90
b = 112.793	β = 90
c = 181.249	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-06-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-06-29
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.2: 2024-10-16
Changes: Structure summary

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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.