6DGS | pdb_00006dgs

Crystal Structure of Leishmania major dihydroorotate dehydrogenase mutant Y142A

• PDB DOI: https://doi.org/10.2210/pdb6DGS/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Leishmania major
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-05-18 Released: 2019-05-29 
• Deposition Author(s): Reis, R.A.G., Pinheiro, M.P., Nonato, M.C.
• Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Leishmania major dihydroorotate dehydrogenase mutant Y142A

Reis, R.A.G., Pinheiro, M.P., Nonato, M.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 77.46 kDa 
• Atom Count: 5,311 
• Modeled Residue Count: 606 
• Deposited Residue Count: 708 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydroorotate dehydrogenase (fumarate)	A, B	354	Leishmania major	Mutation(s): 1  Gene Names: DHODH, LMJF_16_0530 EC: 1.3.98.1
UniProt
Find proteins for Q4QEW7 (Leishmania major) Explore Q4QEW7  Go to UniProtKB:  Q4QEW7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	C [auth A], F [auth B]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
SO4	E [auth A], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A], G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSX	A, B	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.188 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.651	α = 90
b = 140.651	β = 90
c = 68.001	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-05-29 
Deposition Author(s): Reis, R.A.G., Pinheiro, M.P., Nonato, M.C.

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Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	11/23504-9
Sao Paulo Research Foundation (FAPESP)	Brazil	07/08703-0

Revision History  

• Version 1.0: 2019-05-29
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description