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- PDB-1edz: STRUCTURE OF THE NAD-DEPENDENT 5,10-METHYLENETETRAHYDROFOLATE DEH... -

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Basic information

Entry
Database: PDB / ID: 1edz
TitleSTRUCTURE OF THE NAD-DEPENDENT 5,10-METHYLENETETRAHYDROFOLATE DEHYDROGENASE FROM SACCHAROMYCES CEREVISIAE
Components5,10-METHYLENETETRAHYDROFOLATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / nucleotide-binding domain / monofunctional / dehydrogenase / folate
Function / homology
Function and homology information


methylenetetrahydrofolate dehydrogenase (NAD+) / folic acid-containing compound biosynthetic process / methylenetetrahydrofolate dehydrogenase (NAD+) activity / methenyltetrahydrofolate cyclohydrolase activity / methylenetetrahydrofolate dehydrogenase (NADP+) activity / purine nucleobase biosynthetic process / purine nucleotide biosynthetic process / tetrahydrofolate interconversion / one-carbon metabolic process / nucleus / cytosol
Similarity search - Function
Methylenetetrahydrofolate dehydrogenase, NAD-binding domain / 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 / Leucine Dehydrogenase, chain A, domain 1 / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily ...Methylenetetrahydrofolate dehydrogenase, NAD-binding domain / 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 / Leucine Dehydrogenase, chain A, domain 1 / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Methylenetetrahydrofolate dehydrogenase [NAD(+)]
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsMonzingo, A.F. / Breksa, A. / Ernst, S. / Appling, D.R. / Robertus, J.D.
Citation
Journal: Protein Sci. / Year: 2000
Title: The X-ray structure of the NAD-dependent 5,10-methylenetetrahydrofolate dehydrogenase from Saccharomyces cerevisiae.
Authors: Monzingo, A.F. / Breksa, A. / Ernst, S. / Appling, D.R. / Robertus, J.D.
#1: Journal: Proteins / Year: 1996
Title: Crystallization of the NAD-dependent 5,10-methylenetetrahydrofolate dehydrogenase from Saccharomyces cerevisiae
Authors: Monzingo, A.F. / West, M.G. / Schelp, E. / Appling, D.R. / Robertus, J.D.
History
DepositionJan 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5,10-METHYLENETETRAHYDROFOLATE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)36,2851
Polymers36,2851
Non-polymers00
Water39622
1
A: 5,10-METHYLENETETRAHYDROFOLATE DEHYDROGENASE

A: 5,10-METHYLENETETRAHYDROFOLATE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)72,5692
Polymers72,5692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)73.980, 73.980, 161.685
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein 5,10-METHYLENETETRAHYDROFOLATE DEHYDROGENASE


Mass: 36284.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: NAD+ DEPENDENT
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli)
References: UniProt: Q02046, methylenetetrahydrofolate dehydrogenase (NAD+)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: PEG 8000, Tris-HCl, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Details: Monzingo, A.F., (1996) Proteins: Struct., Funct., Genet., 26, 481.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17 %PEG80001reservoir
250 mMTris-HCl1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV1IMAGE PLATEMar 16, 1999
RIGAKU RAXIS IV2IMAGE PLATEMar 22, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 11644 / Num. obs: 11388 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 68.8 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 12
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3 % / Rmerge(I) obs: 0.263 / Num. unique all: 1131 / % possible all: 96.3
Reflection
*PLUS
Num. obs: 10691
Reflection shell
*PLUS
Mean I/σ(I) obs: 12

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
X-PLOR3.851refinement
RefinementResolution: 2.8→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.351 526 -random
Rwork0.26 ---
obs0.265 10132 86.9 %-
all-11659 --
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2511 0 0 22 2533
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.217
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.26 / Rfactor Rfree: 0.35
Solvent computation
*PLUS
Displacement parameters
*PLUS

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