5TSQ | pdb_00005tsq

Crystal structure of IUnH from Leishmania braziliensis in complex with D-Ribose

• PDB DOI: https://doi.org/10.2210/pdb5TSQ/pdb

• Classification: HYDROLASE
• Organism(s): Leishmania braziliensis braziliensis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-10-31 Released: 2016-12-14 
• Deposition Author(s): Bachega, J.F.R., Timmers, L.F.S.M., Dalberto, P.F., Martinelli, L., Pinto, A.F.M., Basso, L.A., Norberto de Souza, O., Santos, D.S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 
  0.169 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.153 (Depositor) 
• R-Value Observed: 
  0.154 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of IUnH from Leishmania braziliensis in complex with D-Ribose

Bachega, J.F.R., Timmers, L.F.S.M., Dalberto, P.F., Martinelli, L., Pinto, A.F.M., Basso, L.A., Norberto de Souza, O., Santos, D.S.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.44 kDa 
• Atom Count: 2,710 
• Modeled Residue Count: 312 
• Deposited Residue Count: 312 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IUnH	A	312	Leishmania braziliensis braziliensis	Mutation(s): 0  Gene Names: LBRM_18_1610 EC: 3.2.2.1
UniProt
Find proteins for A4H9Q9 (Leishmania braziliensis) Explore A4H9Q9  Go to UniProtKB:  A4H9Q9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BDR	C [auth A]	beta-D-ribofuranose C5 H10 O5 HMFHBZSHGGEWLO-TXICZTDVSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free:  0.169 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.153 (Depositor) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.66	α = 90
b = 94.08	β = 90
c = 123.12	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-14 
Deposition Author(s): Bachega, J.F.R., Timmers, L.F.S.M., Dalberto, P.F., Martinelli, L., Pinto, A.F.M., Basso, L.A., Norberto de Souza, O., Santos, D.S.

Revision History  

• Version 1.0: 2016-12-14
  Type: Initial release
  
• Version 1.1: 2016-12-21
  Changes: Structure summary
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-23
  Changes: Structure summary