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- PDB-2fmn: Ala177Val mutant of E. coli Methylenetetrahydrofolate Reductase c... -

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Basic information

Entry
Database: PDB / ID: 2fmn
TitleAla177Val mutant of E. coli Methylenetetrahydrofolate Reductase complex with LY309887
Components5,10-methylenetetrahydrofolate reductase
KeywordsOXIDOREDUCTASE / TIM BARREL / FLAVIN / REDUCTASE
Function / homology
Function and homology information


methylenetetrahydrofolate reductase (NADH) / methylenetetrahydrofolate reductase (NADH) activity / methylenetetrahydrofolate reductase (NAD(P)H) activity / methionine biosynthetic process / tetrahydrofolate interconversion / FAD binding / protein-folding chaperone binding / protein-containing complex / cytosol
Similarity search - Function
5,10-methylenetetrahydrofolate reductase / Methylenetetrahydrofolate reductase-like / Methylenetetrahydrofolate reductase / TIM Barrel - #220 / FAD-linked oxidoreductase-like / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-4HF / FLAVIN-ADENINE DINUCLEOTIDE / 5,10-methylenetetrahydrofolate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsPejchal, R. / Campbell, E. / Guenther, B.D. / Lennon, B.W. / Matthews, R.G. / Ludwig, M.L.
CitationJournal: Biochemistry / Year: 2006
Title: Structural Perturbations in the Ala -> Val Polymorphism of Methylenetetrahydrofolate Reductase: How Binding of Folates May Protect against Inactivation
Authors: Pejchal, R. / Campbell, E. / Guenther, B.D. / Lennon, B.W. / Matthews, R.G. / Ludwig, M.L.
History
DepositionJan 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5,10-methylenetetrahydrofolate reductase
B: 5,10-methylenetetrahydrofolate reductase
C: 5,10-methylenetetrahydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,4379
Polymers102,7323
Non-polymers3,7056
Water5,062281
1
B: 5,10-methylenetetrahydrofolate reductase
hetero molecules

A: 5,10-methylenetetrahydrofolate reductase
B: 5,10-methylenetetrahydrofolate reductase
C: 5,10-methylenetetrahydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,91612
Polymers136,9764
Non-polymers4,9408
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation2_556-x,y,-z+11
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.560, 128.640, 96.744
Angle α, β, γ (deg.)90.00, 120.87, 90.00
Int Tables number5
Space group name H-MC121
DetailsThis entry contains the crystallographic asymmetric unit, which consists of 3 chains. The second part of the biological assembly contains a symmetry related chain B generated by the two fold axis: -x, y, -z. The biological assembly consists of chains A, B, B', and C, where B' is the symmetry related chain B.

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Components

#1: Protein 5,10-methylenetetrahydrofolate reductase


Mass: 34243.902 Da / Num. of mol.: 3 / Mutation: A177V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: metF / Plasmid: pET23B / Production host: Escherichia coli (E. coli)
References: UniProt: P0AEZ1, methylenetetrahydrofolate reductase [NAD(P)H]
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-4HF / N-[(5-{2-[(6R)-2-AMINO-4-OXO-3,4,5,6,7,8-HEXAHYDROPYRIDO[2,3-D]PYRIMIDIN-6-YL]ETHYL}-2-THIENYL)CARBONYL]-L-GLUTAMIC ACID / 6R-2',5'-THIENYL-5,10-DIDEAZATETRAHYDROFOLIC ACID / LY309887


Mass: 449.481 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C19H23N5O6S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.64 Å3/Da / Density % sol: 53.39 %
Crystal growTemperature: 295 K / pH: 6.5
Details: PEG 8000, MAGNESIUM ACETATE, SODIUM CACODYLATE, GLYCEROL, METHYLPENTANEDIOL, LY309887, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→35.8 Å / Num. obs: 62268 / % possible obs: 93.3 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 22.5 Å2
Reflection shellResolution: 2.05→2.18 Å / % possible all: 85.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1B5T

1b5t


Resolution: 2.05→35.78 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 547514.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.25 3161 5.1 %RANDOM
Rwork0.217 ---
obs0.217 62268 93.3 %-
all-66721 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.29 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 34.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å2-3.33 Å2
2--1.49 Å20 Å2
3----1.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.05→35.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6533 0 252 281 7066
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.941.5
X-RAY DIFFRACTIONc_mcangle_it1.632
X-RAY DIFFRACTIONc_scbond_it1.272
X-RAY DIFFRACTIONc_scangle_it1.992.5
LS refinement shellResolution: 2.05→2.18 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.275 455 4.8 %
Rwork0.264 8944 -
obs--85.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3FAD.PARAMFAD.TOP
X-RAY DIFFRACTION44HF.PARAM4HF.TOP

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