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- PDB-7th4: T. thermophilus methylenetetrahydrofolate reductase complex with ... -

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Basic information

Entry
Database: PDB / ID: 7th4
TitleT. thermophilus methylenetetrahydrofolate reductase complex with 5-formyltetrahydrofolate
ComponentsMethylenetetrahydrofolate reductase
KeywordsOXIDOREDUCTASE / TIM barrel / flavin / 5-formyltetrahydrofolate
Function / homology
Function and homology information


methylenetetrahydrofolate reductase (NADH) / methylenetetrahydrofolate reductase (NADH) activity / methionine biosynthetic process / tetrahydrofolate interconversion / FAD binding / cytosol
Similarity search - Function
5,10-methylenetetrahydrofolate reductase / Methylenetetrahydrofolate reductase-like / Methylenetetrahydrofolate reductase / FAD-linked oxidoreductase-like
Similarity search - Domain/homology
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / Chem-FFO / Methylenetetrahydrofolate reductase
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsYamada, K. / Koutmos, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: 5-Formyltetrahydrofolate promotes conformational remodeling in a methylenetetrahydrofolate reductase active site and inhibits its activity.
Authors: Yamada, K. / Mendoza, J. / Koutmos, M.
History
DepositionJan 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Oct 25, 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: Methylenetetrahydrofolate reductase
B: Methylenetetrahydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,78510
Polymers66,1022
Non-polymers2,6838
Water8,017445
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Size exclusion column chromatography with the multi-angle light scattering detector (Igari et al, PLoS (2011))
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.069, 89.545, 161.258
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Methylenetetrahydrofolate reductase


Mass: 33050.887 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: ATCC 27634 / DSM 579 / HB8 / Gene: TTHA0327 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5SLG6, methylenetetrahydrofolate reductase [NAD(P)H]

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Non-polymers , 5 types, 453 molecules

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


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-FFO / N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid / [6S]-5-FORMYL-TETRAHYDROFOLATE / 6S-FOLINIC ACID


Mass: 473.439 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H23N7O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.46 Å3/Da / Density % sol: 50.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1M sodium acetate buffer pH 4.5, 2.5M NaCl, 0.2M lithium sulfate, 1.2% myo-inositol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.45→46.13 Å / Num. obs: 116419 / % possible obs: 99.7 % / Redundancy: 4.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.046 / Rrim(I) all: 0.098 / Net I/σ(I): 10.7
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.979 / Num. unique obs: 5654 / CC1/2: 0.674 / Rpim(I) all: 0.581 / Rrim(I) all: 0.1144 / % possible all: 99.3

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Processing

Software
NameVersionClassification
Aimlessdata scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3APY

3apy


Resolution: 1.45→46.13 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.972 / SU B: 2.851 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1783 5915 5.1 %RANDOM
Rwork0.1311 ---
obs0.1335 110406 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 173.48 Å2 / Biso mean: 32.344 Å2 / Biso min: 15.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å2-0 Å2
2--0.52 Å2-0 Å2
3----0.3 Å2
Refinement stepCycle: final / Resolution: 1.45→46.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4596 0 288 445 5329
Biso mean--28.06 39.46 -
Num. residues----582
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0124921
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174758
X-RAY DIFFRACTIONr_angle_refined_deg1.5871.656681
X-RAY DIFFRACTIONr_angle_other_deg0.561.56610812
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9295586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.52219.21291
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0815787
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1211560
X-RAY DIFFRACTIONr_chiral_restr0.080.2597
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025580
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021232
X-RAY DIFFRACTIONr_rigid_bond_restr7.33234921
LS refinement shellResolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 455 -
Rwork0.267 7979 -
all-8434 -
obs--99.29 %

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