7L9R | pdb_00007l9r

Crystal Structure of a putative deoxyhypusine synthase from Entamoeba histolytica

PDB DOI: https://doi.org/10.2210/pdb7L9R/pdb

Classification: TRANSFERASE
Organism(s): Entamoeba histolytica HM-1:IMSS
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-01-04 Released: 2021-02-10
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.218 (Depositor), 0.222 (DCC)
R-Value Work:
0.187 (Depositor), 0.192 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of a putative deoxyhypusine synthase from Entamoeba histolytica

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

To be published.

Macromolecule Content

Total Structure Weight: 79.17 kDa
Atom Count: 4,537
Modeled Residue Count: 562
Deposited Residue Count: 704
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxyhypusine synthase, putative	A, B	352	Entamoeba histolytica HM-1:IMSS	Mutation(s): 0 Gene Names: EHI_098350
UniProt
Find proteins for C4LXB8 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM)) Explore C4LXB8 Go to UniProtKB: C4LXB8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C4LXB8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.218 (Depositor), 0.222 (DCC)
R-Value Work: 0.187 (Depositor), 0.192 (DCC)
R-Value Observed: 0.189 (Depositor)

Diffraction Data:

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.9	α = 90
b = 85.9	β = 90
c = 424.52	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing
PHENIX	model building
BUCCANEER	model building
Coot	model building

Structure Validation

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Entry History

Deposition Data

Released Date: 2021-02-10

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2021-02-10
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, Refinement description

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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.