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- PDB-6v6y: Crystal Structure of T. thermophilus methylenetetrahydrofolate de... -

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Basic information

Entry
Database: PDB / ID: 6v6y
TitleCrystal Structure of T. thermophilus methylenetetrahydrofolate dehydrogenase (MTHFD)
ComponentsBifunctional protein FolD
KeywordsOXIDOREDUCTASE / Amino-acid biosynthesis / Histidine biosynthesis / Hydrolase / Methionine biosynthesis / Multifunctional enzyme / NADP / One-carbon metabolism / Purine biosynthesis
Function / homology
Function and homology information


methylenetetrahydrofolate dehydrogenase (NADP+) / methenyltetrahydrofolate cyclohydrolase / methenyltetrahydrofolate cyclohydrolase activity / methylenetetrahydrofolate dehydrogenase (NADP+) activity / methionine biosynthetic process / histidine biosynthetic process / purine nucleotide biosynthetic process / tetrahydrofolate interconversion
Similarity search - Function
Tetrahydrofolate dehydrogenase/cyclohydrolase signature 2. / Tetrahydrofolate dehydrogenase/cyclohydrolase, conserved site / Tetrahydrofolate dehydrogenase/cyclohydrolase / Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain / Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain / Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain / Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Bifunctional protein FolD
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15201566872 Å
AuthorsMaiello, F. / Coelho, C. / Gallo, G. / Sucharski, F. / Hardy, L. / Wurtele, M.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation11/50963-4 Brazil
Brazilian National Council for Scientific and Technological Development448833/2014-0 Brazil
CitationJournal: Plos One / Year: 2020
Title: Crystal structure of Thermus thermophilus methylenetetrahydrofolate dehydrogenase and determinants of thermostability.
Authors: Maiello, F. / Gallo, G. / Coelho, C. / Sucharski, F. / Hardy, L. / Wurtele, M.
History
DepositionDec 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 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

Downloads & links

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Assembly

Deposited unit
A: Bifunctional protein FolD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9852
Polymers30,2411
Non-polymers7431
Water1,08160
1
A: Bifunctional protein FolD
hetero molecules

A: Bifunctional protein FolD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9694
Polymers60,4822
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Buried area4930 Å2
ΔGint-5 kcal/mol
Surface area23080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.357, 121.357, 59.620
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Bifunctional protein FolD / / Methylenetetrahydrofolate dehydrogenase (MTHFD)


Mass: 30241.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: DSM 579
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / Gene: folD, TTHA1120 / Plasmid: pQtev / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q5SJ94, methylenetetrahydrofolate dehydrogenase (NADP+), methenyltetrahydrofolate cyclohydrolase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 4.19 Å3/Da / Density % sol: 70.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 800 mM Potassium sodium tartrate, 100 mM HEPES buffer pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4587 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 5, 2018 / Details: Toroidal bendable
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4587 Å / Relative weight: 1
ReflectionResolution: 2.152→39.42 Å / Num. obs: 25688 / % possible obs: 92.32 % / Redundancy: 8.53 % / Biso Wilson estimate: 45.8749638437 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.087 / Net I/σ(I): 19.87
Reflection shellResolution: 2.152→2.229 Å / Redundancy: 2.96 % / Mean I/σ(I) obs: 0.85 / Num. unique obs: 1122 / CC1/2: 0.433 / Rrim(I) all: 1.431 / % possible all: 38.23

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.12-2829-000phasing
PHENIX1.12-2829-000refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P2O

3p2o


Resolution: 2.15201566872→39.4219349912 Å / SU ML: 0.290097408121 / Cross valid method: FREE R-VALUE / σ(F): 1.34350028871 / Phase error: 29.7360547215
RfactorNum. reflection% reflection
Rfree0.243890427109 1283 5.01544114773 %
Rwork0.213132527796 --
obs0.214668092329 25581 92.3501805054 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 51.1275158399 Å2
Refinement stepCycle: LAST / Resolution: 2.15201566872→39.4219349912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2127 0 48 60 2235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007852085521312217
X-RAY DIFFRACTIONf_angle_d0.9752960553193024
X-RAY DIFFRACTIONf_chiral_restr0.0531833663331356
X-RAY DIFFRACTIONf_plane_restr0.00626947034189387
X-RAY DIFFRACTIONf_dihedral_angle_d4.580219007071353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15201566872-2.23820.439916147107670.3796814117031212X-RAY DIFFRACTION42.0447074293
2.2382-2.340.3640375812761360.3143644810422591X-RAY DIFFRACTION89.8517298188
2.34-2.46340.2957791806691520.2756973108212881X-RAY DIFFRACTION99.377457405
2.4634-2.61770.2769874350671530.255713711612898X-RAY DIFFRACTION100
2.6177-2.81970.2901300737551530.2442957434212918X-RAY DIFFRACTION99.9674479167
2.8197-3.10340.2908724028381530.2397396799062907X-RAY DIFFRACTION99.9020568071
3.1034-3.55220.2340286582241540.2195505195132922X-RAY DIFFRACTION99.9675008125
3.5522-4.47440.227169629571560.183772551072954X-RAY DIFFRACTION100
4.4744-39.42193499120.1998432834211590.1822980646663015X-RAY DIFFRACTION99.2495309568

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