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- PDB-8wfc: N5, N10-methylenetetrahydrofolate dehydrogenase/cyclohydrolase -

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Basic information

Entry
Database: PDB / ID: 8wfc
TitleN5, N10-methylenetetrahydrofolate dehydrogenase/cyclohydrolase
ComponentsBifunctional protein FolD
KeywordsOXIDOREDUCTASE / Apo structure
Function / homology
Function and homology information


methylenetetrahydrofolate dehydrogenase (NADP+) / methenyltetrahydrofolate cyclohydrolase / methenyltetrahydrofolate cyclohydrolase activity / methylenetetrahydrofolate dehydrogenase (NADP+) activity / methionine biosynthetic process / L-histidine biosynthetic process / purine nucleotide biosynthetic process / tetrahydrofolate interconversion / cytosol
Similarity search - Function
Tetrahydrofolate dehydrogenase/cyclohydrolase signature 1. / Tetrahydrofolate dehydrogenase/cyclohydrolase signature 2. / Tetrahydrofolate dehydrogenase/cyclohydrolase, conserved site / Tetrahydrofolate dehydrogenase/cyclohydrolase / Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain / Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain / Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain / Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Bifunctional protein FolD
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsHwang, J. / Lee, J.H. / Do, H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)PM23030 Korea, Republic Of
CitationJournal: Crystals / Year: 2023
Title: Crystal Structure and Sequence Analysis of N5, N10-Methylenetetrahydrofolate Dehydrogenase/Cyclohydrolase Enzyme from Porphyromonas gingivalis
Authors: Im, S. / Do, H. / Hwang, J. / Shim, Y.S. / Lee, J.H.
History
DepositionSep 19, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional protein FolD


Theoretical massNumber of molelcules
Total (without water)31,9741
Polymers31,9741
Non-polymers00
Water2,936163
1
A: Bifunctional protein FolD

A: Bifunctional protein FolD


Theoretical massNumber of molelcules
Total (without water)63,9482
Polymers63,9482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/41
Buried area2830 Å2
ΔGint-12 kcal/mol
Surface area24320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.681, 110.681, 69.781
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Space group name HallP4cw2c
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+1/4
#8: -y,-x,-z+3/4
Components on special symmetry positions
IDModelComponents
11A-451-

HOH

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Components

#1: Protein Bifunctional protein FolD


Mass: 31973.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Gene: folD / Production host: Escherichia coli (E. coli) / References: UniProt: Q7MVE9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.48 Å3/Da / Density % sol: 64.62 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / Details: Sodium Potassium phosphate, MPD

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 27821 / % possible obs: 99.9 % / Redundancy: 26 % / Biso Wilson estimate: 35.71 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 59.67
Reflection shellResolution: 2.05→2.09 Å / Rmerge(I) obs: 0.304 / Num. unique obs: 1347 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5refinement
PHENIX1.14_3260refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→35 Å / SU ML: 0.2019 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.4468 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2378 1413 5.09 %
Rwork0.215 26360 -
obs0.2161 27773 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.01 Å2
Refinement stepCycle: LAST / Resolution: 2.05→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2152 0 0 163 2315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01062188
X-RAY DIFFRACTIONf_angle_d1.13132968
X-RAY DIFFRACTIONf_chiral_restr0.2796356
X-RAY DIFFRACTIONf_plane_restr0.0058382
X-RAY DIFFRACTIONf_dihedral_angle_d25.0545828
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.120.28811420.25392576X-RAY DIFFRACTION99.96
2.12-2.210.2761320.23332597X-RAY DIFFRACTION100
2.21-2.310.27171480.23722583X-RAY DIFFRACTION100
2.31-2.430.25011170.24022619X-RAY DIFFRACTION100
2.43-2.580.28451360.2362623X-RAY DIFFRACTION100
2.58-2.780.24461400.24052617X-RAY DIFFRACTION100
2.78-3.060.24721420.23472624X-RAY DIFFRACTION99.93
3.06-3.50.23491580.21852630X-RAY DIFFRACTION99.93
3.5-4.410.21411250.18412694X-RAY DIFFRACTION99.86
4.41-350.21931730.20332797X-RAY DIFFRACTION99.17

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