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- PDB-4jki: Crystal Structure of N10-Formyltetrahydrofolate Synthetase with Z... -

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Basic information

Entry
Database: PDB / ID: 4jki
TitleCrystal Structure of N10-Formyltetrahydrofolate Synthetase with ZD9331, Formylphosphate, and ADP
ComponentsFormate--tetrahydrofolate ligase
KeywordsLIGASE/LIGASE INHIBITOR / Ligase / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsCeleste, L.R. / Lovelace, L.L. / Lebioda, L.
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
DepositionMar 9, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionMar 20, 2013ID: 3SIN
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Sep 9, 2020Group: Derived calculations / Structure summary / Category: struct / struct_site
Item: _struct.title / _struct_site.pdbx_auth_asym_id ..._struct.title / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 20, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)121,2039
Polymers120,0242
Non-polymers1,1797
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7200 Å2
ΔGint-102 kcal/mol
Surface area36840 Å2
MethodPISA
2
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)242,40518
Polymers240,0484
Non-polymers2,35714
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area16510 Å2
ΔGint-214 kcal/mol
Surface area71580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.373, 162.373, 258.074
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 5 - 558 / Label seq-ID: 5 - 558

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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, moorella, Moth_0109 / Plasmid: pAlter-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Y1
References: UniProt: Q2RM91, formate-tetrahydrofolate ligase

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Non-polymers , 5 types, 105 molecules

#2: 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
#3: Chemical ChemComp-XPO / formyl phosphate


Mass: 126.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH3O5P
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.73 Å3/Da / Density % sol: 54.9 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 75 mM Potassium Maleate Buffer pH 7.0-8.5, 1 mM dithiothreitol, 40% Ammonium Sulfate, 20% PEG 1000, vapor diffusion, hanging drop, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 12, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.58→50 Å / % possible obs: 91.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.049 / Net I/σ(I): 10.6
Reflection shell
Resolution (Å)Rmerge(I) obsDiffraction-ID% possible all
2.58-2.670.571131.6
2.67-2.780.494187.4
2.78-2.910.389197.3
2.91-3.060.247198.5
3.06-3.250.163199.4
3.25-3.50.109199.8
3.5-3.850.063199.9
3.85-4.410.037199.8
4.41-5.560.024199.6
5.56-500.017197.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SIN

3sin
PDB Unreleased entry


Resolution: 2.6→32.03 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.921 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 26.813 / SU ML: 0.267 / SU R Cruickshank DPI: 1.5515 / Cross valid method: THROUGHOUT / ESU R: 1.486 / ESU R Free: 0.337 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24922 1820 5 %RANDOM
Rwork0.18637 ---
obs0.18952 34498 89.28 %-
all-61740 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.146 Å2
Baniso -1Baniso -2Baniso -3
1-1.42 Å21.42 Å20 Å2
2--1.42 Å20 Å2
3----4.61 Å2
Refinement stepCycle: LAST / Resolution: 2.6→32.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8207 0 72 98 8377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0198419
X-RAY DIFFRACTIONr_bond_other_d0.0010.028114
X-RAY DIFFRACTIONr_angle_refined_deg1.5311.98511454
X-RAY DIFFRACTIONr_angle_other_deg0.83318626
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25451110
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.83224.654318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.981151344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5021540
X-RAY DIFFRACTIONr_chiral_restr0.0810.21350
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219589
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021763
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 32854 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.595→2.663 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 74 -
Rwork0.387 1335 -
obs--47.46 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.38060.3176-0.35080.4881-0.33170.3611-0.10230.16290.00860.03490.1240.02280.0232-0.078-0.02180.2226-0.1-0.00550.3095-0.06180.4445-0.667934.069156.7591
20.26680.22790.12380.39120.12550.2284-0.03280.0464-0.01620.11840.0649-0.0196-0.00970.0092-0.03220.2549-0.00290.00920.2343-0.06980.48657.38231.686878.8169
30.3772-0.2277-0.37620.17150.22060.4247-0.0832-0.0273-0.11060.05790.05760.0170.0498-0.03920.02560.2387-0.0923-0.01420.2842-0.02650.587612.258328.453755.3158
40.49290.30080.04010.3885-0.31130.636-0.3310.1798-0.0784-0.24110.2979-0.15920.0559-0.25560.03310.3375-0.30590.00510.4916-0.14390.3274-0.688430.599925.8099
52.26880.00660.6061.62750.4891.5854-0.8080.3405-0.1052-0.59550.8723-0.5844-0.06260.0859-0.06420.5962-0.5410.27730.6499-0.34060.239510.916330.353611.9994
60.91660.5578-0.24730.43590.11420.8409-0.27190.54410.2325-0.16160.33040.11050.0938-0.2555-0.05860.1964-0.1736-0.06420.49820.01060.33381.81444.125733.6706
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 299
2X-RAY DIFFRACTION2A300 - 517
3X-RAY DIFFRACTION3A518 - 559
4X-RAY DIFFRACTION4B5 - 417
5X-RAY DIFFRACTION5B418 - 522
6X-RAY DIFFRACTION6B523 - 559

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