3JTW | pdb_00003jtw

Crystal structure of Putative dihydrofolate reductase (YP_805003.1) from PEDIOCOCCUS PENTOSACEUS ATCC 25745 at 1.90 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3JTW/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pediococcus pentosaceus ATCC 25745
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-09-14 Released: 2009-10-06 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.225 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

Crystal structure of Putative dihydrofolate reductase (YP_805003.1) from PEDIOCOCCUS PENTOSACEUS ATCC 25745 at 1.90 A resolution

Joint Center for Structural Genomics (JCSG)

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 Evidence: gel filtration

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 41.93 kDa 
• Atom Count: 3,232 
• Modeled Residue Count: 348 
• Deposited Residue Count: 356 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A, B	178	Pediococcus pentosaceus ATCC 25745	Mutation(s): 0  Gene Names: PEPE_1533, YP_805003.1
UniProt
Find proteins for Q03E11 (Pediococcus pentosaceus (strain ATCC 25745 / CCUG 21536 / LMG 10740 / 183-1w)) Explore Q03E11  Go to UniProtKB:  Q03E11

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], G [auth B], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
UNL	C [auth A]	Unknown ligand LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.225 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33JTW

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.759	α = 90
b = 83.314	β = 90
c = 65.059	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-06 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-10-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-27
  Changes: Data collection, Refinement description, Structure summary