3BWB | pdb_00003bwb

Crystal structure of the apo form of spermidine synthase from Trypanosoma cruzi at 2.5 A resolution

PDB DOI: https://doi.org/10.2210/pdb3BWB/pdb

Classification: TRANSFERASE
Organism(s): Trypanosoma cruzi strain CL Brener
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-01-08 Released: 2008-04-01
Deposition Author(s): Bosch, J., Hol, W.G.J., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.248 (Depositor), 0.254 (DCC)
R-Value Work:
0.198 (Depositor), 0.204 (DCC)
R-Value Observed:
0.201 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3BWB

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of spermidine synthase from Trypanosoma cruzi.

Bosch, J., Hol, W.G.J.

To be published.

Macromolecule Content

Total Structure Weight: 69.05 kDa
Atom Count: 4,671
Modeled Residue Count: 571
Deposited Residue Count: 608
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spermidine synthase	A, B	304	Trypanosoma cruzi strain CL Brener	Mutation(s): 0 Gene Names: Tc00.1047053510339.50 EC: 2.5.1.16
UniProt
Find proteins for Q4DA73 (Trypanosoma cruzi (strain CL Brener)) Explore Q4DA73 Go to UniProtKB: Q4DA73
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4DA73
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.248 (Depositor), 0.254 (DCC)
R-Value Work: 0.198 (Depositor), 0.204 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.669	α = 90
b = 96.996	β = 106.33
c = 69.649	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
XDS	data reduction
XSCALE	data scaling
SHELXD	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-04-01

Deposition Author(s):

Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Revision History (Full details and data files)

Version 1.0: 2008-04-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.2: 2024-11-13
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.