6OTE | pdb_00006ote

Crystal Structure of Seryl-tRNA synthetase (SerRS) from Cryptosporidium parvum complexed with L-Serylsulfamoyl Adenosine

PDB DOI: https://doi.org/10.2210/pdb6OTE/pdb

Classification: LIGASE
Organism(s): Cryptosporidium parvum Iowa II
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-05-03 Released: 2019-05-15
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free:
0.253 (Depositor), 0.255 (DCC)
R-Value Work:
0.208 (Depositor), 0.213 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of Seryl-tRNA synthetase (SerRS) from Cryptosporidium parvum complexed with L-Serylsulfamoyl Adenosine

Dranow, D.M., Abendroth, J., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 66.09 kDa
Atom Count: 3,072
Modeled Residue Count: 409
Deposited Residue Count: 572
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, cytoplasmic	A	572	Cryptosporidium parvum Iowa II	Mutation(s): 0 Gene Names: cgd8_4720 EC: 6.1.1.11
UniProt
Find proteins for Q5CVB3 (Cryptosporidium parvum (strain Iowa II)) Explore Q5CVB3 Go to UniProtKB: Q5CVB3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5CVB3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SSA (Subject of Investigation/LOI) Query on SSA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE C₁₃ H₁₉ N₇ O₈ S HQXFJGONGJPTLZ-YTMOPEAISA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free: 0.253 (Depositor), 0.255 (DCC)
R-Value Work: 0.208 (Depositor), 0.213 (DCC)
R-Value Observed: 0.211 (Depositor)

Diffraction Data: https://doi.org/10.18430/m36ote

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.21	α = 90
b = 92.21	β = 90
c = 257.18	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
MoRDa	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2019-05-15

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2019-05-15
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description

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.