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- PDB-1ee9: CRYSTAL STRUCTURE OF THE NAD-DEPENDENT 5,10-METHYLENETETRAHYDROFO... -

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Basic information

Entry
Database: PDB / ID: 1ee9
TitleCRYSTAL STRUCTURE OF THE NAD-DEPENDENT 5,10-METHYLENETETRAHYDROFOLATE DEHYDROGENASE FROM SACCHAROMYCES CEREVISIAE COMPLEXED WITH NAD
Components5,10-METHYLENETETRAHYDROFOLATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / NUCLEOTIDE-BINDING DOMAIN / PROTEIN-NAD COMPLEX / MONOFUNCTIONAL / DEHYDROGENASE / FOLATE
Function / homology
Function and homology information


methylenetetrahydrofolate dehydrogenase (NAD+) / folic acid-containing compound biosynthetic process / methylenetetrahydrofolate dehydrogenase (NAD+) activity / purine nucleobase biosynthetic process / methylenetetrahydrofolate dehydrogenase (NADP+) activity / purine nucleotide biosynthetic process / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Methylenetetrahydrofolate dehydrogenase [NAD(+)]
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 3 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 31, 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 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5,10-METHYLENETETRAHYDROFOLATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9482
Polymers36,2851
Non-polymers6631
Water1086
1
A: 5,10-METHYLENETETRAHYDROFOLATE DEHYDROGENASE
hetero molecules

A: 5,10-METHYLENETETRAHYDROFOLATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8964
Polymers72,5692
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)73.600, 73.600, 161.601
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
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli)
References: UniProt: Q02046, methylenetetrahydrofolate dehydrogenase (NAD+)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 3.01 Å3/Da / Density % sol: 59.2 %
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

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 9, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. all: 8474 / Num. obs: 8474 / % possible obs: 81.3 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 11.3
Reflection shellResolution: 2.9→3 Å / Redundancy: 3 % / Rmerge(I) obs: 0.578 / Num. unique all: 726 / % possible all: 73
Reflection shell
*PLUS
Mean I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851refinement
RefinementMethod to determine structure: DIFFERENCE FOURIER / Resolution: 3→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.36 408 -random
Rwork0.248 ---
all0.254 7391 --
obs0.254 7391 78.4 %-
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2511 0 44 6 2561
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.004
X-RAY DIFFRACTIONx_angle_deg1.216
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.25 / Rfactor obs: 0.25 / Rfactor Rwork: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS

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