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- PDB-7th5: Thermus thermophilus methylenetetrahydrofolate reductase -

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Basic information

Entry
Database: PDB / ID: 7th5
TitleThermus thermophilus methylenetetrahydrofolate reductase
ComponentsMethylenetetrahydrofolate reductase
KeywordsOXIDOREDUCTASE / TIM barrel / flavin
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 / TIM Barrel - #220 / FAD-linked oxidoreductase-like / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Methylenetetrahydrofolate reductase
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 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)67,7196
Polymers66,1022
Non-polymers1,6174
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
  • 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
Buried area5300 Å2
ΔGint-52 kcal/mol
Surface area23520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.496, 91.288, 130.261
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#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]
#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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.72 Å3/Da / Density % sol: 54.79 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris-HCl pH 8.5, 3M NaCl

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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: Jun 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.09→47.07 Å / Num. obs: 42742 / % possible obs: 98.7 % / Redundancy: 3.9 % / CC1/2: 0.993 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.069 / Rrim(I) all: 0.138 / Net I/σ(I): 7.6
Reflection shellResolution: 2.09→2.15 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.621 / Num. unique obs: 2924 / CC1/2: 0.674 / Rpim(I) all: 0.316 / Rrim(I) all: 0.621 / % possible all: 88.4

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Processing

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

3apy


Resolution: 2.09→47.07 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.074 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.185 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2239 2157 5.1 %RANDOM
Rwork0.1817 ---
obs0.1838 40515 98.68 %-
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: 218.89 Å2 / Biso mean: 34.665 Å2 / Biso min: 10.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å2-0 Å20 Å2
2--1.27 Å2-0 Å2
3----2.12 Å2
Refinement stepCycle: final / Resolution: 2.09→47.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4547 0 160 156 4863
Biso mean--34.39 36.36 -
Num. residues----576
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0124771
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174551
X-RAY DIFFRACTIONr_angle_refined_deg1.6181.6466470
X-RAY DIFFRACTIONr_angle_other_deg0.5321.55810439
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2255573
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.43319.357280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.0615774
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.4271557
X-RAY DIFFRACTIONr_chiral_restr0.0760.2585
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025375
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021165
LS refinement shellResolution: 2.094→2.149 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 139 -
Rwork0.274 2750 -
all-2889 -
obs--91.42 %

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