3LSS | pdb_00003lss

Trypanosoma brucei seryl-tRNA synthetase in complex with ATP

PDB DOI: https://doi.org/10.2210/pdb3LSS/pdb

Classification: LIGASE
Organism(s): Trypanosoma brucei
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-02-12 Released: 2010-03-02
Deposition Author(s): Larson, E.T., Merritt, E.A., Medical Structural Genomics of Pathogenic Protozoa (MSGPP)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.195 (Depositor), 0.200 (DCC)
R-Value Work:
0.168 (Depositor), 0.180 (DCC)
R-Value Observed:
0.169 (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 Seryl-tRNA synthetase from the eukaryotic parasite Trypanosoma brucei.

Larson, E.T., Zhang, L., Napuli, A., Mueller, N., 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: 109.95 kDa
Atom Count: 7,683
Modelled Residue Count: 906
Deposited Residue Count: 968
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Seryl-tRNA synthetase	A, B	484	Trypanosoma brucei	Mutation(s): 0 Gene Names: SerRS, Tb11.02.5020 EC: 6.1.1.11
UniProt
Find proteins for Q384V4 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1)) Explore Q384V4 Go to UniProtKB: Q384V4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q384V4
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
MLI Query on MLI Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.195 (Depositor), 0.200 (DCC)
R-Value Work: 0.168 (Depositor), 0.180 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 175.652	α = 90
b = 175.652	β = 90
c = 248.518	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-03-02

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: 2010-03-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description

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Trypanosoma brucei seryl-tRNA synthetase in complex with ATP

X-ray crystal structure of Seryl-tRNA synthetase from the eukaryotic parasite Trypanosoma brucei.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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