3M4P | pdb_00003m4p

Entamoeba histolytica asparaginyl-tRNA synthetase (AsnRS) in complex with asparaginyl-adenylate

PDB DOI: https://doi.org/10.2210/pdb3M4P/pdb

Classification: LIGASE
Organism(s): Entamoeba histolytica
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-03-11 Released: 2010-03-23
Deposition Author(s): Larson, E.T., Merritt, E.A., Medical Structural Genomics of Pathogenic Protozoa (MSGPP)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.83 Å
R-Value Free:
0.247 (Depositor), 0.244 (DCC)
R-Value Work:
0.199 (Depositor), 0.199 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

X-ray crystal structure of asparaginyl-tRNA synthetase from the eukaryotic human pathogen Entamoeba histolytica.

Larson, E.T., Kim, J.E., Napuli, A., Kelley, A., Castaneda, L., Verlinde, C.L.M.J., Van Voorhis, W.C., Buckner, F.S., Fan, E., Hol, W.G.J., Merritt, E.A.

To be published.

Macromolecule Content

Total Structure Weight: 213.21 kDa
Atom Count: 14,100
Modeled Residue Count: 1,734
Deposited Residue Count: 1,824
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Asparaginyl-tRNA synthetase, putative	A, B, C, D	456	Entamoeba histolytica	Mutation(s): 0 Gene Names: 159.m00096, EHI_126920 EC: 6.1.1.22
UniProt
Find proteins for C4LWW8 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM)) Explore C4LWW8 Go to UniProtKB: C4LWW8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C4LWW8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4AD Query on 4AD Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain N [auth C] SDF format, chain R [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] MOL2 format, chain R [auth D] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C] mmCIF format, chain R [auth D]	E [auth A], J [auth B], N [auth C], R [auth D]	4-AMINO-1,4-DIOXOBUTAN-2-AMINIUM ADENOSINE-5'-MONOPHOSPHATE C₁₄ H₂₁ N₇ O₉ P BZHVCXQAFQWXPZ-VWJPMABRSA-O		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain R [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain R [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain U [auth D] SDF format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain H [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D] mmCIF format, chain H [auth A]	F [auth A] G [auth A] H [auth A] K [auth B] L [auth B] F [auth A], G [auth A], H [auth A], K [auth B], L [auth B], M [auth B], O [auth C], P [auth C], Q [auth C], S [auth D], T [auth D], U [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain V [auth D] MOL2 format, chain I [auth A] MOL2 format, chain V [auth D] mmCIF format, chain I [auth A] mmCIF format, chain V [auth D]	I [auth A], V [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain V [auth D] Interactions & Density Focus chain I [auth A] Focus chain V [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.83 Å
R-Value Free: 0.247 (Depositor), 0.244 (DCC)
R-Value Work: 0.199 (Depositor), 0.199 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.426	α = 90
b = 58.816	β = 90.45
c = 181.259	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
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: 2010-03-23

Deposition Author(s):

Larson, E.T.

Merritt, E.A.

Medical Structural Genomics of Pathogenic Protozoa (MSGPP)

Revision History (Full details and data files)

Version 1.0: 2010-03-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description