Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 108.78 kDa 
• Atom Count: 7097 
• Modelled Residue Count: 865 
• Deposited Residue Count: 971 
• Unique protein chains: 2

2XDQ

Dark Operative Protochlorophyllide Oxidoreductase (ChlN-ChlB)2 Complex

• PDB DOI: 10.2210/pdb2XDQ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermosynechococcus vestitus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-05-06 Released: 2010-06-16 
• Deposition Author(s): Broecker, M.J., Schomburg, S., Heinz, D.W., Jahn, D., Schubert, W.-D., Moser, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.257 
• R-Value Work: 0.201 
• R-Value Observed: 0.204 

Literature

Crystal Structure of the Nitrogenase-Like Dark Operative Protochlorophyllide Oxidoreductase Catalytic Complex (Chln/Chlb)2.

Broecker, M.J., Schomburg, S., Heinz, D.W., Jahn, D., Schubert, W.-D., Moser, J.

(2010) J Biol Chem 285: 27336

• PubMed: 20558746 
• DOI: 10.1074/jbc.M110.126698
• Primary Citation of Related Structures:  
  2XDQ


• PubMed Abstract: 
  

During (bacterio)chlorophyll biosynthesis of many photosynthetically active organisms, dark operative protochlorophyllide oxidoreductase (DPOR) catalyzes the two-electron reduction of ring D of protochlorophyllide to form chlorophyllide. DPOR is composed of the subunits ChlL, ChlN, and ChlB. Homodimeric ChlL(2) bearing an intersubunit [4Fe-4S] cluster is an ATP-dependent reductase transferring single electrons to the heterotetrameric (ChlN/ChlB)(2) complex. The latter contains two intersubunit [4Fe-4S] clusters and two protochlorophyllide binding sites, respectively. Here we present the crystal structure of the catalytic (ChlN/ChlB)(2) complex of DPOR from the cyanobacterium Thermosynechococcus elongatus at a resolution of 2.4 A. Subunits ChlN and ChlB exhibit a related architecture of three subdomains each built around a central, parallel beta-sheet surrounded by alpha-helices. The (ChlN/ChlB)(2) crystal structure reveals a [4Fe-4S] cluster coordinated by an aspartate oxygen alongside three cysteine ligands. Two equivalent substrate binding sites enriched in aromatic residues for protochlorophyllide substrate binding are located at the interface of each ChlN/ChlB half-tetramer. The complete octameric (ChlN/ChlB)(2)(ChlL(2))(2) complex of DPOR was modeled based on the crystal structure and earlier functional studies. The electron transfer pathway via the various redox centers of DPOR to the substrate is proposed.

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Organizational Affiliation: 

Institut für Mikrobiologie, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE SUBUNIT N	A	460	Thermosynechococcus vestitus	Mutation(s): 0  EC: 1.18 (PDB Primary Data), 1.3.7.7 (UniProt)
UniProt
Find proteins for Q8DGH2 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DGH2  Go to UniProtKB:  Q8DGH2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LIGHT-INDEPENDENT PROTOCHLOROPHYLLIDE REDUCTASE SUBUNIT B	B	511	Thermosynechococcus vestitus	Mutation(s): 0  EC: 1.18 (PDB Primary Data), 1.3.7.7 (UniProt)
UniProt
Find proteins for Q8DGC6 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DGC6  Go to UniProtKB:  Q8DGC6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4	C [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-VKOJMFJBAC
SO4	E [auth B], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MGX	D [auth A]	1-METHYLGUANIDINE C2 H7 N3 CHJJGSNFBQVOTG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.257 
• R-Value Work: 0.201 
• R-Value Observed: 0.204 
• Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 192.095	α = 90
b = 192.095	β = 90
c = 132.504	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-05-06 
• Released Date: 2010-06-16 
Deposition Author(s): Broecker, M.J., Schomburg, S., Heinz, D.W., Jahn, D., Schubert, W.-D., Moser, J.

Revision History  

• Version 1.0: 2010-06-16
  Type: Initial release
  
• Version 1.1: 2015-04-29
  Changes: Data collection, Version format compliance
• Version 1.2: 2017-04-19
  Changes: Data collection
• Version 1.3: 2019-05-08
  Changes: Data collection, Experimental preparation