3I83 | pdb_00003i83

Crystal structure of 2-dehydropantoate 2-reductase from Methylococcus capsulatus

• PDB DOI: https://doi.org/10.2210/pdb3I83/pdb

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


• Deposited: 2009-07-09 Released: 2009-07-21 
• Deposition Author(s): Bonanno, J.B., Gilmore, M., Bain, K.T., Chang, S., Sampathkumar, P., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.227 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Literature

Crystal structure of 2-dehydropantoate 2-reductase from Methylococcus capsulatus

Bonanno, J.B., Gilmore, M., Bain, K.T., Chang, S., Sampathkumar, P., Sauder, J.M., Burley, S.K., Almo, S.C.

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)

Macromolecule Content 

• Total Structure Weight: 68.96 kDa 
• Atom Count: 4,702 
• Modeled Residue Count: 597 
• Deposited Residue Count: 640 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-dehydropantoate 2-reductase	A, B	320	Methylococcus capsulatus	Mutation(s): 0  Gene Names: MCA2523, panE EC: 1.1.1.169
UniProt
Find proteins for Q604L6 (Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)) Explore Q604L6  Go to UniProtKB:  Q604L6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACY	C [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.227 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.851	α = 90
b = 79.179	β = 90
c = 100.626	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-21 
Deposition Author(s): Bonanno, J.B., Gilmore, M., Bain, K.T., Chang, S., Sampathkumar, P., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-07-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-02-21
  Changes: Data collection, Database references