3HXJ | pdb_00003hxj

Crystal Structure of Pyrrolo-quinoline quinone (PQQ_DH) from Methanococcus maripaludis, Northeast Structural Genomics Consortium Target MrR86

• PDB DOI: https://doi.org/10.2210/pdb3HXJ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Methanococcus maripaludis C7
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-06-20 Released: 2009-08-25 
• Deposition Author(s): Forouhar, F., Chen, Y., Seetharaman, J., Sahdev, S., Xiao, R., Ciccosanti, C., Foote, E.L., Zhao, L., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.242 (Depositor), 0.265 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Literature

Northeast Structural Genomics Consortium Target MrR86

Forouhar, F., Chen, Y., Seetharaman, J., Sahdev, S., Xiao, R., Ciccosanti, C., Foote, E.L., Zhao, L., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L.

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 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 149.81 kDa 
• Atom Count: 10,202 
• Modeled Residue Count: 1,189 
• Deposited Residue Count: 1,320 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyrrolo-quinoline quinone	A, B, C, D	330	Methanococcus maripaludis C7	Mutation(s): 0  Gene Names: MmarC7 1297, MmarC7_1297
UniProt
Find proteins for A6VIT4 (Methanococcus maripaludis (strain C7 / ATCC BAA-1331)) Explore A6VIT4  Go to UniProtKB:  A6VIT4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth B], F [auth C], G [auth C], H [auth C], I [auth C], J [auth D], K [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.242 (Depositor), 0.265 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.225	α = 90
b = 66.958	β = 115.29
c = 112.082	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
DENZO	data reduction
SCALEPACK	data scaling
SnB	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-25 
Deposition Author(s): Forouhar, F., Chen, Y., Seetharaman, J., Sahdev, S., Xiao, R., Ciccosanti, C., Foote, E.L., Zhao, L., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2009-08-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary