3IC3 | pdb_00003ic3

Structure of a putative pyruvate dehydrogenase from the photosynthetic bacterium Rhodopseudomonas palustrus CGA009

• PDB DOI: https://doi.org/10.2210/pdb3IC3/pdb

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


• Deposited: 2009-07-17 Released: 2009-09-22 
• Deposition Author(s): Cuff, M.E., Tesar, C., Jedrzejczak, R., Mckinlay, J.B., Harwood, C.S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.195 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Literature

Structure of a putative pyruvate dehydrogenase from the photosynthetic bacterium Rhodopseudomonas palustrus CGA009

Cuff, M.E., Tesar, C., Jedrzejczak, R., Mckinlay, J.B., Harwood, C.S., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 46.83 kDa 
• Atom Count: 3,564 
• Modeled Residue Count: 376 
• Deposited Residue Count: 404 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative pyruvate dehydrogenase	A, B, C, D	101	Rhodopseudomonas palustris	Mutation(s): 0  Gene Names: JGI_07::RPA2865, RPA2865
UniProt
Find proteins for Q6N5V5 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore Q6N5V5  Go to UniProtKB:  Q6N5V5

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BGC	G [auth B]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
PO4	J [auth C], L [auth D], M [auth D]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	E [auth A], F [auth A], I [auth B], N [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
K	H [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
NA	K [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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: 1.80 Å
• R-Value Free:  0.195 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.7	α = 90
b = 64.995	β = 90
c = 116.89	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-22 
Deposition Author(s): Cuff, M.E., Tesar, C., Jedrzejczak, R., Mckinlay, J.B., Harwood, C.S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-09-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2024-11-06
  Changes: Data collection, Database references, Structure summary