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- PDB-6pey: MTHFR with mutation Asp120Ala -

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Basic information

Entry
Database: PDB / ID: 6pey
TitleMTHFR with mutation Asp120Ala
ComponentsMethylenetetrahydrofolate reductase
KeywordsOXIDOREDUCTASE / METHYLTRANSFERASE / 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 / peroxidase activity / 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 / Methylenetetrahydrofolate reductase / 5,10-methylenetetrahydrofolate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsGallagher, E.L. / Gurney, L.A. / Frasco, F.G. / Trimmer, E. / Bolen, R.L. / Collins, K. / Garland, E. / Halloran, J. / Handley-Pendelton, J. / Hernandez, V. ...Gallagher, E.L. / Gurney, L.A. / Frasco, F.G. / Trimmer, E. / Bolen, R.L. / Collins, K. / Garland, E. / Halloran, J. / Handley-Pendelton, J. / Hernandez, V. / Leffler, S. / Perez, A. / Soares, A. / Stojanoff, V. / Williams, D.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM111244 United States
Department of Energy (DOE, United States)DE-SC0012704 United States
Department of Energy (DOE, United States)KP1605010 United States
CitationJournal: To be published
Title: Examination of Asp120Ala a Chemically Important Novel Mutation in the Enzyme Mthylenetetrahydrofolate Reductase
Authors: Gallagher, E.L. / Gurney, L.A. / Frasco, F.G. / Bolen, R.L. / Garland, E. / Halloran, J. / Handley-Pendelton, J. / Hernandez, V. / Leffler, S. / Perez, A. / Soares, A. / Stojanoff, V. / Williams, D.
History
DepositionJun 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Methylenetetrahydrofolate reductase
B: Methylenetetrahydrofolate reductase
C: Methylenetetrahydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,8726
Polymers102,5163
Non-polymers2,3573
Water543
1
A: Methylenetetrahydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9572
Polymers34,1721
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methylenetetrahydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9572
Polymers34,1721
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Methylenetetrahydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9572
Polymers34,1721
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: Methylenetetrahydrofolate reductase
C: Methylenetetrahydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9154
Polymers68,3442
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-31 kcal/mol
Surface area23460 Å2
MethodPISA
5
B: Methylenetetrahydrofolate reductase
hetero molecules

B: Methylenetetrahydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9154
Polymers68,3442
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6810 Å2
ΔGint-34 kcal/mol
Surface area23150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.747, 127.744, 95.456
Angle α, β, γ (deg.)90.000, 120.900, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12B
22C
13C
23A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 300
2114B1 - 300
1124B1 - 300
2124C1 - 300
1134C1 - 300
2134A1 - 300

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Methylenetetrahydrofolate reductase


Mass: 34171.844 Da / Num. of mol.: 3 / Mutation: D120A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: C3SIT0, UniProt: P0AEZ1*PLUS, 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 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.82 Å3/Da / Density % sol: 56.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: MembFac / PH range: 4.6-8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9202 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9202 Å / Relative weight: 1
ReflectionResolution: 2.87→28.97 Å / Num. obs: 22352 / % possible obs: 98.24 % / Observed criterion σ(F): 0.708 / Redundancy: 3.4 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 8.6
Reflection shellResolution: 2.87→2.94 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.984 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1392 / CC1/2: 0.43 / % possible all: 83.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1zp3

1zp3


Resolution: 2.88→28.97 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / SU B: 18.202 / SU ML: 0.326 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.379 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2364 1131 4.8 %RANDOM
Rwork0.1882 ---
obs0.1905 22352 98.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 233.5 Å2 / Biso mean: 74.348 Å2 / Biso min: 34.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0 Å20.03 Å2
2---0.03 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 2.88→28.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6469 0 159 3 6631
Biso mean--117.77 59.97 -
Num. residues----848
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0136779
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176126
X-RAY DIFFRACTIONr_angle_refined_deg1.5251.6439244
X-RAY DIFFRACTIONr_angle_other_deg1.2321.57514118
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9715842
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.97221.74339
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.238151036
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3091547
X-RAY DIFFRACTIONr_chiral_restr0.0570.2929
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027645
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021443
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A4164MEDIUM POSITIONAL0.540.5
1A4164MEDIUM THERMAL10.552
2B4066MEDIUM POSITIONAL0.560.5
2B4066MEDIUM THERMAL9.172
3C3986MEDIUM POSITIONAL0.540.5
3C3986MEDIUM THERMAL9.272
LS refinement shellResolution: 2.882→2.957 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 91 -
Rwork0.334 1392 -
all-1483 -
obs--85.13 %

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