5THX | pdb_00005thx

Crystal Structure of a ferredoxin NADP+ reductase from Neisseria gonorrhoeae with bound NADP and FAD

• PDB DOI: https://doi.org/10.2210/pdb5THX/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Neisseria gonorrhoeae MIA_2011_03-10
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-09-30 Released: 2016-10-19 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.188 (Depositor), 0.188 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.160 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of a ferredoxin NADP+ reductase from Neisseria gonorrhoeae with bound NADP and FAD

Phan, J.N., Dranow, D.M., Mayclin, S.J., Lorimer, D.D., Edwards, T.E.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 32 kDa 
• Atom Count: 2,611 
• Modeled Residue Count: 257 
• Deposited Residue Count: 266 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferredoxin--NADP reductase	A	266	Neisseria gonorrhoeae MIA_2011_03-10	Mutation(s): 0  Gene Names: M736_00365

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	D [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
NAP	B [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.188 (Depositor), 0.188 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35THX

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.01	α = 90
b = 60.01	β = 90
c = 158.27	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-10-19 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2016-10-19
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description