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

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Basic information

Entry
Database: PDB / ID: 3fst
TitleCrystal Structure of Escherichia coli Methylenetetrahydrofolate Reductase Mutant Phe223Leu at pH 7.4
Components5,10-methylenetetrahydrofolate reductase
KeywordsOXIDOREDUCTASE / TIM BARREL / FLAVIN / REDUCTASE / 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
FLAVIN-ADENINE DINUCLEOTIDE / MESO-ERYTHRITOL / 5,10-methylenetetrahydrofolate reductase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.65 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)105,31210
Polymers102,5463
Non-polymers2,7677
Water8,215456
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)140,28012
Polymers136,7274
Non-polymers3,5538
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation2_656-x+1,y,-z+11
identity operation1_555x,y,z1
Buried area25170 Å2
ΔGint-183 kcal/mol
Surface area61840 Å2
Unit cell
Length a, b, c (Å)103.057, 128.157, 98.314
Angle α, β, γ (deg.)90.00, 121.97, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-382-

HOH

21C-407-

HOH

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Components

#1: Protein 5,10-methylenetetrahydrofolate reductase


Mass: 34181.836 Da / Num. of mol.: 3 / Mutation: F223L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: metF, b3941, JW3913 / Plasmid: pDTL2 / Production host: Escherichia coli (E. coli)
References: UniProt: P0AEZ1, methylenetetrahydrofolate reductase [NAD(P)H]
#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-MRY / MESO-ERYTHRITOL


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


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 456 / 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: 2.69 Å3/Da / Density % sol: 54.2 %
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: 1.65→34.95 Å / Num. obs: 129128 / % possible obs: 99.6 % / Redundancy: 3.75 % / Rmerge(I) obs: 0.045 / Χ2: 0.93 / Scaling rejects: 3658
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.65-1.713.670.3632.447641129430.96100
1.71-1.783.740.216448412129480.95100
1.78-1.863.750.1665.348428128920.96100
1.86-1.963.760.1346.448745129490.93100
1.96-2.083.770.0978.548721129060.87100
2.08-2.243.780.07211.649178129820.84100
2.24-2.463.770.0561549077129200.8499.9
2.46-2.823.790.0442049775129450.8899.6
2.82-3.553.790.03724.849828129350.9199.6
3.55-34.953.670.03530.647911127081.297

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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: 1.65→32.144 Å / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.842 / SU ML: 0.27 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.228 6474 5.02 %
Rwork0.21 --
obs0.211 129047 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.791 Å2 / ksol: 0.376 e/Å3
Displacement parametersBiso max: 332.09 Å2 / Biso mean: 34.577 Å2 / Biso min: 12.64 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.65→32.144 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6458 0 190 456 7104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076814
X-RAY DIFFRACTIONf_angle_d1.1269332
X-RAY DIFFRACTIONf_chiral_restr0.0691044
X-RAY DIFFRACTIONf_plane_restr0.0091193
X-RAY DIFFRACTIONf_dihedral_angle_d23.5432571
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 (%)
1.65-1.7090.286640.241227112935100
1.709-1.7770.266640.2161228312947100
1.777-1.8580.2396340.2051225412888100
1.858-1.9560.266370.2051230912946100
1.956-2.0790.2256490.1931225812907100
2.079-2.2390.2256060.1911237512981100
2.239-2.4640.2126520.1961226612918100
2.464-2.8210.2366760.2071225912935100
2.821-3.5530.2056460.21122681291499
3.553-32.150.2096460.196120301267697
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)
10.88220.1634-0.49831.3204-0.61721.8161-0.01020.1437-0.0263-0.16660.0788-0.05550.0673-0.0882-0.05290.1624-0.01160.03870.1396-0.01880.144931.7554-20.17921.9953
20.9039-0.2184-0.45640.2333-0.00840.837-0.0428-0.00720.01690.0250.0087-0.01420.0007-0.01280.02880.21350.01930.00680.1388-0.00720.12218.98112.508518.4664
31.43140.80480.05951.5786-0.03141.3159-0.36240.3237-0.1148-0.54560.3023-0.12410.1122-0.06040.04890.4326-0.18920.11430.207-0.01770.081656.57929.167925.6596
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain a
2X-RAY DIFFRACTION2chain c
3X-RAY DIFFRACTION3chain e

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