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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.238 (Depositor), 0.235 (DCC)
R-Value Work:
0.215 (Depositor)
R-Value Observed:
0.216 (Depositor)

Starting Model: in silico
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This is version 1.0 of the entry. See complete history.

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

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7MVE9
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.238 (Depositor), 0.235 (DCC)
R-Value Work: 0.215 (Depositor)
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

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-08-07

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.