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- PDB-2eo2: Solution structure of the insertion region (510-573) of FTHFS dom... -

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Entry
Database: PDB / ID: 2eo2
TitleSolution structure of the insertion region (510-573) of FTHFS domain from mouse methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1-like protein
ComponentsAdult male hypothalamus cDNA, RIKEN full-length enriched library, clone:A230045M11 product:weakly similar to C1-tetrahydrofolate synthase
KeywordsOXIDOREDUCTASE / Fthfsdc1 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Metabolism of folate and pterines / 10-formyltetrahydrofolate biosynthetic process / formate-tetrahydrofolate ligase / formate-tetrahydrofolate ligase activity / embryonic neurocranium morphogenesis / formate metabolic process / methenyltetrahydrofolate cyclohydrolase activity / embryonic viscerocranium morphogenesis / methylenetetrahydrofolate dehydrogenase (NADP+) activity / folic acid-containing compound metabolic process ...Metabolism of folate and pterines / 10-formyltetrahydrofolate biosynthetic process / formate-tetrahydrofolate ligase / formate-tetrahydrofolate ligase activity / embryonic neurocranium morphogenesis / formate metabolic process / methenyltetrahydrofolate cyclohydrolase activity / embryonic viscerocranium morphogenesis / methylenetetrahydrofolate dehydrogenase (NADP+) activity / folic acid-containing compound metabolic process / tetrahydrofolate interconversion / neural tube closure / one-carbon metabolic process / protein homodimerization activity / mitochondrion / ATP binding / cytosol
Similarity search - Function
Helicase, Ruva Protein; domain 3 - #770 / Formate-tetrahydrofolate ligase, FTHFS / Formate-tetrahydrofolate ligase, FTHFS, conserved site / Formate--tetrahydrofolate ligase / Formate--tetrahydrofolate ligase signature 1. / Formate--tetrahydrofolate ligase signature 2. / Tetrahydrofolate dehydrogenase/cyclohydrolase / Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain / Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain / Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain ...Helicase, Ruva Protein; domain 3 - #770 / Formate-tetrahydrofolate ligase, FTHFS / Formate-tetrahydrofolate ligase, FTHFS, conserved site / Formate--tetrahydrofolate ligase / Formate--tetrahydrofolate ligase signature 1. / Formate--tetrahydrofolate ligase signature 2. / 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 / Helicase, Ruva Protein; domain 3 / NAD(P)-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Monofunctional C1-tetrahydrofolate synthase, mitochondrial / Monofunctional C1-tetrahydrofolate synthase, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsKurosaki, C. / Nagashima, T. / Yoshida, M. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the insertion region (510-573) of FTHFS domain from mouse methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1-like protein
Authors: Kurosaki, C. / Nagashima, T. / Yoshida, M. / Hayashi, F. / Yokoyama, S.
History
DepositionMar 28, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
A: Adult male hypothalamus cDNA, RIKEN full-length enriched library, clone:A230045M11 product:weakly similar to C1-tetrahydrofolate synthase


Theoretical massNumber of molelcules
Total (without water)7,8981
Polymers7,8981
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations, structures with the lowest energy, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Adult male hypothalamus cDNA, RIKEN full-length enriched library, clone:A230045M11 product:weakly similar to C1-tetrahydrofolate synthase


Mass: 7897.887 Da / Num. of mol.: 1 / Fragment: UNP residues 510-573
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: cell free protein synthesis / Gene: Mthfd1l / Plasmid: P061211-10 / References: UniProt: Q8CAL0, UniProt: Q3V3R1*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 1.16mM 13C, 15N-labeled protein; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe20031121Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.9817Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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