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- PDB-1sou: NMR structure of Aquifex aeolicus 5,10-methenyltetrahydrofolate s... -

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Basic information

Entry
Database: PDB / ID: 1sou
TitleNMR structure of Aquifex aeolicus 5,10-methenyltetrahydrofolate synthetase: Northeast Structural Genomics Consortium Target QR46
Components5,10-methenyltetrahydrofolate synthetase
KeywordsLIGASE / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


5-formyltetrahydrofolate cyclo-ligase / 5-formyltetrahydrofolate cyclo-ligase activity / folic acid-containing compound biosynthetic process / tetrahydrofolate interconversion / ATP binding / metal ion binding
Similarity search - Function
NagB/RpiA/CoA transferase-like / 5-formyltetrahydrofolate cyclo-ligase / 5-formyltetrahydrofolate cyclo-ligase family / 5-formyltetrahydrofolate cyclo-ligase-like domain superfamily / NagB/RpiA transferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5-formyltetrahydrofolate cyclo-ligase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodSOLUTION NMR / MOLECULAR DYNAMICS, SIMULATED ANNEALING
AuthorsCort, J.R. / Chiang, Y. / Acton, T. / Wu, M. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: NMR structure of Aquifex aeolicus 5,10-methenyltetrahydrofolate synthetase: Northeast Structural Genomics Consortium Target QR46
Authors: Cort, J.R. / Chiang, Y. / Acton, T. / Wu, M. / Montelione, G.T. / Kennedy, M.A.
History
DepositionMar 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5,10-methenyltetrahydrofolate synthetase


Theoretical massNumber of molelcules
Total (without water)22,3611
Polymers22,3611
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 29structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1combination of factors

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Components

#1: Protein 5,10-methenyltetrahydrofolate synthetase


Mass: 22361.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: aq_1731 / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMGK
References: UniProt: O67621, 5-formyltetrahydrofolate cyclo-ligase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1334D 13C-separated NOESY
141HNHA

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM 5,10-methenyltetrahydrofolate synthetase U-15N,13C; 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02% NaN3 pH 6.5 95% H2O, 5% D2O95% H2O/5% D2O
20.5 mM 5,10-methenyltetrahydrofolate synthetase U-15N,5%-13C; 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02% NaN3 pH 6.5 95% H2O, 5% D2O95% H2O/5% D2O
31 mM 5,10-methenyltetrahydrofolate synthetase U-15N,13C; 20 mM MES, 100 mM NaCl, 5 mM CaCl2, 10 mM DTT, 0.02% NaN3 pH 6.5 100% D2O100% D2O
Sample conditionsIonic strength: 0.115 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYVarianUNITY6001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA7503
Varian INOVAVarianINOVA8004

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Processing

NMR software
NameVersionDeveloperClassification
NIH-XPLOR2.0.4AT Brunger, GM Clore, J Kuszewski, CD Schwieters, N Tjandrarefinement
CNS1.1AT Brungerrefinement
VNMR6.1CVarian Inc.collection
Felix97MSI/Biosymdata analysis
TALOSG Cornilescu, F Delaglio, A Baxdata analysis
RefinementMethod: MOLECULAR DYNAMICS, SIMULATED ANNEALING / Software ordinal: 1
Details: FINAL REFINEMENT IN EXPLICIT SOLVENT WITH LEONARD-JONES AND ELECTROSTATIC POTENTIALS. BACKBONE AND SIDECHAIN ASSIGNMENTS WERE DETERMINED MANUALLY FROM TRIPLE-RESONANCE NMR DATA. NOE DISTANCE ...Details: FINAL REFINEMENT IN EXPLICIT SOLVENT WITH LEONARD-JONES AND ELECTROSTATIC POTENTIALS. BACKBONE AND SIDECHAIN ASSIGNMENTS WERE DETERMINED MANUALLY FROM TRIPLE-RESONANCE NMR DATA. NOE DISTANCE RESTRAINTS WERE DERIVED MANUALLY FROM NOESY DATA. THE STRUCTURE IS BASED ON 1235 RESTRAINTS: 938 NOE DISTANCE RESTRAINTS, 112 H-BOND RESTRAINTS (56 H-BONDS), AND 185 DIHEDRAL RESTRAINTS. PHI DIHEDRAL RESTRAINTS WERE DERIVED FROM THE HNHA EXPERIMENT AND TALOS. PSI DIHEDRAL RESTRAINTS WERE DERIVED FROM NOE RATIOS, SECONDARY STRUCTURE PROPENSITIES EVIDENT IN PRELIMINARY STRUCTURES, ALPHA CARBON CHEMICAL SHIFTS, AND TALOS. RESIDUES 1-2 AND 182-194 ARE UNSTRUCTURED TERMINI IN THIS ENSEMBLE.
NMR representativeSelection criteria: combination of factors
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 29 / Conformers submitted total number: 20

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