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- PDB-4iol: N10-formyltetrahydrofolate synthetase from Moorella thermoacetica... -

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Basic information

Entry
Database: PDB / ID: 4iol
TitleN10-formyltetrahydrofolate synthetase from Moorella thermoacetica with ADP/ZD9 and XPO
ComponentsFormate--tetrahydrofolate ligase
KeywordsLIGASE/LIGASE INHIBITOR / alpha/beta / enzyme / LIGASE-LIGASE INHIBITOR complex
Function / homology
Function and homology information


formate-tetrahydrofolate ligase / formate-tetrahydrofolate ligase activity / tetrahydrofolate interconversion / ATP binding
Similarity search - Function
Formyltetrahydrofolate synthetase; domain 3 / Formyltetrahydrofolate synthetase, domain 3 / Domain 2, N(10)-formyltetrahydrofolate synthetase / Domain 2, N(10)-formyltetrahydrofolate synthetase / Formate-tetrahydrofolate ligase, FTHFS / Formate-tetrahydrofolate ligase, FTHFS, conserved site / Formate--tetrahydrofolate ligase / Formate--tetrahydrofolate ligase signature 1. / Formate--tetrahydrofolate ligase signature 2. / P-loop containing nucleotide triphosphate hydrolases ...Formyltetrahydrofolate synthetase; domain 3 / Formyltetrahydrofolate synthetase, domain 3 / Domain 2, N(10)-formyltetrahydrofolate synthetase / Domain 2, N(10)-formyltetrahydrofolate synthetase / Formate-tetrahydrofolate ligase, FTHFS / Formate-tetrahydrofolate ligase, FTHFS, conserved site / Formate--tetrahydrofolate ligase / Formate--tetrahydrofolate ligase signature 1. / Formate--tetrahydrofolate ligase signature 2. / P-loop containing nucleotide triphosphate hydrolases / Roll / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / formyl phosphate / Chem-ZD9 / Formate--tetrahydrofolate ligase
Similarity search - Component
Biological speciesMoorella thermoacetica (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.563 Å
AuthorsStec, B.
CitationJournal: Protein Sci. / Year: 2012
Title: Mechanism of N10-formyltetrahydrofolate synthetase derived from complexes with intermediates and inhibitors.
Authors: Celeste, L.R. / Chai, G. / Bielak, M. / Minor, W. / Lovelace, L.L. / Lebioda, L.
History
DepositionJan 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 0THIS ENTRY 4IOL REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA R3PZXSF DETERMINED ...THIS ENTRY 4IOL REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA R3PZXSF DETERMINED BY AUTHORS OF THE PDB ENTRY 3SIN: L.R. CELESTE, G. CHAI, M. BIELAK, W. MINOR, L.L. LOVELACE, L. LEBIODA
Remark 200AUTHOR USED THE SF DATA FROM ENTRY 3SIN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Formate--tetrahydrofolate ligase
B: Formate--tetrahydrofolate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,63010
Polymers120,0242
Non-polymers1,6068
Water2,972165
1
A: Formate--tetrahydrofolate ligase
B: Formate--tetrahydrofolate ligase
hetero molecules

A: Formate--tetrahydrofolate ligase
B: Formate--tetrahydrofolate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,26020
Polymers240,0484
Non-polymers3,21216
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area18140 Å2
ΔGint-230 kcal/mol
Surface area73250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.370, 160.370, 258.074
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-775-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Formate--tetrahydrofolate ligase / Formyltetrahydrofolate synthetase / FHS / FTHFS


Mass: 60011.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moorella thermoacetica (bacteria) / Strain: ATCC 39073 / Gene: fhs, Moth_0109 / Production host: Escherichia coli (E. coli)
References: UniProt: Q2RM91, formate-tetrahydrofolate ligase

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Non-polymers , 5 types, 173 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-ZD9 / 2,7-dimethyl-6-[(prop-1-yn-1-ylamino)methyl]quinazolin-4(3H)-one


Mass: 241.288 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H15N3O
#5: Chemical ChemComp-XPO / formyl phosphate


Mass: 126.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH3O5P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

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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: 2.66 Å3/Da / Density % sol: 53.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 18 to 22% (w/v) PEG 6-8K, 0.2M AS, 1 mM DTT, 75 mM KMB pH 7.0-8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.56→122.3 Å / Num. obs: 79627 / % possible obs: 91.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 9.4

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SIN

3sin
PDB Unreleased entry


Resolution: 2.563→122.3 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.906 / SU B: 14.909 / SU ML: 0.304 / Cross valid method: THROUGHOUT / ESU R Free: 0.38 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27916 1821 5 %RANDOM
Rwork0.18994 ---
obs0.19442 34496 88.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.713 Å2
Baniso -1Baniso -2Baniso -3
1-1.23 Å20.61 Å20 Å2
2--1.23 Å20 Å2
3----1.84 Å2
Refinement stepCycle: LAST / Resolution: 2.563→122.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8390 0 99 165 8654
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0198631
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.561.99411708
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.52351112
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.04624.345336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.462151468
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0361550
X-RAY DIFFRACTIONr_chiral_restr0.0950.21356
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216388
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.563→2.63 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 51 -
Rwork0.374 1034 -
obs--36.15 %

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