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- PDB-3fsu: Crystal Structure of Escherichia coli Methylenetetrahydrofolate R... -

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Basic information

Entry
Database: PDB / ID: 3fsu
TitleCrystal Structure of Escherichia coli Methylenetetrahydrofolate Reductase Double Mutant Phe223LeuGlu28Gln complexed with methyltetrahydrofolate
Components5,10-methylenetetrahydrofolate reductase
KeywordsOXIDOREDUCTASE / TIM BARREL / FLAVIN / REDUCTASE / METHYLTETRAHYDROFOLATE / Amino-acid biosynthesis / FAD / Flavoprotein / Methionine biosynthesis / NAD / NADP
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
5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / MESO-ERYTHRITOL / 5,10-methylenetetrahydrofolate reductase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsTanner, J.J.
CitationJournal: Biochemistry / Year: 2009
Title: Functional role for the conformationally mobile phenylalanine 223 in the reaction of methylenetetrahydrofolate reductase from Escherichia coli.
Authors: Lee, M.N. / Takawira, D. / Nikolova, A.P. / Ballou, D.P. / Furtado, V.C. / Phung, N.L. / Still, B.R. / Thorstad, M.K. / Tanner, J.J. / Trimmer, E.E.
History
DepositionJan 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 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 1.3Sep 6, 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
C: 5,10-methylenetetrahydrofolate reductase
E: 5,10-methylenetetrahydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,03610
Polymers102,5433
Non-polymers3,4947
Water7,206400
1
A: 5,10-methylenetetrahydrofolate reductase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)141,46213
Polymers136,7234
Non-polymers4,7399
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation2_656-x+1,y,-z+11
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.913, 127.906, 97.606
Angle α, β, γ (deg.)90.000, 121.730, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-393-

HOH

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Components

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Protein , 1 types, 3 molecules ACE

#1: Protein 5,10-methylenetetrahydrofolate reductase


Mass: 34180.852 Da / Num. of mol.: 3 / Mutation: F223L,E28Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: metF, b3941, JW3913 / Plasmid: pEETQL4 / Production host: Escherichia coli (E. coli)
References: UniProt: P0AEZ1, methylenetetrahydrofolate reductase [NAD(P)H]

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Non-polymers , 5 types, 407 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-C2F / 5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID


Mass: 459.456 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H25N7O6
#4: Chemical ChemComp-MRY / MESO-ERYTHRITOL


Mass: 122.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O4
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 2.66 Å3/Da / Density % sol: 53.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5
Details: 100 mM sodium cacodylate buffer pH 5.0- 5.5, 225 mM Li2SO4, 5 % ethanol and 10 - 12 % PEG 4000, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Jun 1, 2008
RadiationMonochromator: beamline 4.2.2 optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→43.71 Å / Num. obs: 117437 / % possible obs: 99.8 % / Redundancy: 3.75 % / Rmerge(I) obs: 0.033 / Χ2: 0.96 / Scaling rejects: 3332
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.7-1.763.440.2833.141136116681.1299.8
1.76-1.833.760.1665.744406117671.04100
1.83-1.913.770.1267.344506117791.04100
1.91-2.023.780.099.944397117030.97100
2.02-2.143.780.06912.744560117290.9399.9
2.14-2.313.790.05515.644636117210.8999.9
2.31-2.543.820.0422045119117560.86100
2.54-2.913.820.03126.945262117680.87100
2.91-3.663.820.0233745527117970.999.9
3.66-43.713.760.02444.944712117491.0398.7

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Processing

Software
NameVersionClassificationNB
d*TREK9.9.1LDzdata processing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing
RefinementStarting model: PDB ENTRY 1zp4

1zp4


Resolution: 1.7→43.707 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.851 / SU ML: 0.25 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.22 5867 5 %
Rwork0.197 --
obs0.198 117404 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.514 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso max: 253.76 Å2 / Biso mean: 31.971 Å2 / Biso min: 11.17 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→43.707 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6459 0 238 400 7097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066866
X-RAY DIFFRACTIONf_angle_d1.0979401
X-RAY DIFFRACTIONf_chiral_restr0.0671046
X-RAY DIFFRACTIONf_plane_restr0.0091200
X-RAY DIFFRACTIONf_dihedral_angle_d23.0742602
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.7610.2865900.2381107611666100
1.761-1.8310.2355780.21118911767100
1.831-1.9150.2415910.1931118811779100
1.915-2.0160.2245780.1871112511703100
2.016-2.1420.2095750.1821115411729100
2.142-2.3070.2215610.1881116011721100
2.307-2.5390.2276120.1951113911751100
2.539-2.9070.2315940.21117111765100
2.907-3.6620.2065900.2011120511795100
3.662-43.7220.1985980.181111301172899
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.67710.0446-0.35030.9751-0.35091.5705-0.00860.105-0.0479-0.15910.0524-0.04660.0822-0.0412-0.03480.156-0.01180.02790.1113-0.02350.108531.7862-20.259921.8811
20.988-0.2046-0.41510.1683-0.020.7547-0.03290.0210.0133-0.00830.0065-0.01580.0017-0.0150.02350.19410.0116-0.00170.11270.00740.09579.237412.269618.3626
31.2090.7579-0.02281.8506-0.27660.7543-0.33780.3003-0.0681-0.56050.2663-0.19270.09110.01320.04040.3971-0.17340.10470.2239-0.02770.101956.52899.453725.2886
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain a
2X-RAY DIFFRACTION2chain c
3X-RAY DIFFRACTION3chain e

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