8WFC | pdb_00008wfc

N5, N10-methylenetetrahydrofolate dehydrogenase/cyclohydrolase

• PDB DOI: https://doi.org/10.2210/pdb8WFC/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Porphyromonas gingivalis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-09-19 Released: 2024-08-07 
• Deposition Author(s): Hwang, J., Lee, J.H., Do, H.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: in silico

Literature

Crystal Structure and Sequence Analysis of N5, N10-Methylenetetrahydrofolate Dehydrogenase/Cyclohydrolase Enzyme from Porphyromonas gingivalis

Im, S., Do, H., Hwang, J., Shim, Y.S., Lee, J.H.

(2023) Crystals (Basel) 13

• DOI: https://doi.org/10.3390/cryst13101489

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

Macromolecule Content 

• Total Structure Weight: 31.97 kDa 
• Atom Count: 2,315 
• Modeled Residue Count: 285 
• Deposited Residue Count: 296 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional protein FolD	A	296	Porphyromonas gingivalis	Mutation(s): 0  Gene Names: folD EC: 1.5.1.5 (UniProt), 3.5.4.9 (UniProt)
UniProt
Find proteins for Q7MVE9 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83)) Explore Q7MVE9  Go to UniProtKB:  Q7MVE9

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.681	α = 90
b = 110.681	β = 90
c = 69.781	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-07 
Deposition Author(s): Hwang, J., Lee, J.H., Do, H.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	PM23030

Revision History  

• Version 1.0: 2024-08-07
  Type: Initial release