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

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Basic information

Entry
Database: PDB / ID: 4iok
TitleN10-formyltetrahydrofolate synthetase from Moorella thermoacetica with ADP, XPO
ComponentsFormate--tetrahydrofolate ligase
KeywordsLIGASE / alpha/beta / enzyme
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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL / formyl phosphate / Formate--tetrahydrofolate ligase
Similarity search - Component
Biological speciesMoorella thermoacetica (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.497 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_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 0THIS ENTRY 4IOK REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA R3RBOSF DETERMINED ...THIS ENTRY 4IOK REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA R3RBOSF DETERMINED BY AUTHORS OF THE PDB ENTRY 3RBO: L.R. CELESTE, G. CHAI, M. BIELAK, W. MINOR, L.L. LOVELACE, L. LEBIODA
Remark 200AUTHOR USED THE SF DATA FROM ENTRY 3RBO.

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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)121,86413
Polymers120,0242
Non-polymers1,84011
Water4,684260
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)243,72726
Polymers240,0484
Non-polymers3,67922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area20340 Å2
ΔGint-215 kcal/mol
Surface area70510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.170, 212.976, 53.444
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-801-

HOH

21B-812-

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 , 6 types, 271 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / 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-XPO / formyl phosphate


Mass: 126.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH3O5P
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-TOE / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL


Mass: 164.200 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H16O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.16 Å3/Da / Density % sol: 43.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 38 to 46% (w/v) saturated ammonium sulfate (AS), 1 mM DTT, and 1 to 3.5% (w/v) PEG 1000 or PEG 1450, in 50 - 75 mM KMB (pH 7.0 - 8.0), 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: 2.497→106.49 Å / Num. obs: 37221 / % possible obs: 91.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.085
Reflection shellResolution: 2.497→2.59 Å / % possible all: 64.8

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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 3RBO

3rbo
PDB Unreleased entry


Resolution: 2.497→106.49 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.888 / SU B: 10.422 / SU ML: 0.233 / Cross valid method: THROUGHOUT / ESU R Free: 0.384 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25876 3242 10 %RANDOM
Rwork0.16424 ---
obs0.17349 29139 87.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.291 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20 Å2
2---2.71 Å20 Å2
3---3.42 Å2
Refinement stepCycle: LAST / Resolution: 2.497→106.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8390 0 113 260 8763
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0198640
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6161.99411705
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1851112
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.2124.345336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.07151468
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8741550
X-RAY DIFFRACTIONr_chiral_restr0.1030.21354
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216370
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: 2.497→2.562 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 123 -
Rwork0.192 1305 -
obs--54.09 %

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