5W4C | pdb_00005w4c

Crystal structure of thioredoxin reductase from Cryptococcus neoformans in complex with FAD (FO conformation)

• PDB DOI: https://doi.org/10.2210/pdb5W4C/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Cryptococcus neoformans var. grubii H99
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-06-09 Released: 2018-06-13 
• Deposition Author(s): Bravo-Chaucanes, C.P., Valadares, N.F., Felipe, M.S.S., Barbosa, J.A.R.G.
• Funding Organization(s): Brazilian National Council for Scientific and Technological Development (CNPq), FAPDF/CNPq

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of thioredoxin reductase from Cryptococcus neoformans in complex with FAD (FO conformation)

Bravo-Chaucanes, C.P., Valadares, N.F., Felipe, M.S.S., Barbosa, J.A.R.G.

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: 81.87 kDa 
• Atom Count: 5,574 
• Modelled Residue Count: 694 
• Deposited Residue Count: 742 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin reductase	A, B	371	Cryptococcus neoformans var. grubii H99	Mutation(s): 0  Gene Names: CNAG_05847 EC: 1.8.1.9
UniProt
Find proteins for J9VRX9 (Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487)) Explore J9VRX9  Go to UniProtKB:  J9VRX9

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A], H [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
PEG	E [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	D [auth A], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	G [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	F [auth A], J [auth B], K [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.14	α = 90
b = 108.828	β = 90
c = 70.354	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-06-13 
Deposition Author(s): Bravo-Chaucanes, C.P., Valadares, N.F., Felipe, M.S.S., Barbosa, J.A.R.G.

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Funding Organization	Location	Grant Number
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	564007/2010-2
FAPDF/CNPq	Brazil	193000569/2009

Revision History  

• Version 1.0: 2018-06-13
  Type: Initial release
  
• Version 1.1: 2019-04-17
  Changes: Author supporting evidence, Data collection
• Version 1.2: 2020-01-08
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary