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- PDB-4jim: Native Crystal Structure of N10-Formyltetrahydrofolate Synthetase -

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Basic information

Entry
Database: PDB / ID: 4jim
TitleNative Crystal Structure of N10-Formyltetrahydrofolate Synthetase
ComponentsFormate--tetrahydrofolate ligase
KeywordsLIGASE
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
2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL / Formate--tetrahydrofolate ligase
Similarity search - Component
Biological speciesMoorella thermoacetica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 6, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionMar 20, 2013ID: 3PZX
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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)121,28513
Polymers120,0242
Non-polymers1,26111
Water9,944552
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8440 Å2
ΔGint-170 kcal/mol
Surface area37900 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)242,57026
Polymers240,0484
Non-polymers2,52222
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_554x-y+1/3,-y+2/3,-z-1/31
Buried area18140 Å2
ΔGint-366 kcal/mol
Surface area74540 Å2
MethodPISA
3
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)242,57026
Polymers240,0484
Non-polymers2,52222
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area19830 Å2
ΔGint-348 kcal/mol
Surface area72850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.192, 161.192, 256.903
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-816-

HOH

21A-901-

HOH

31A-957-

HOH

41B-718-

HOH

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

#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
#2: Chemical ChemComp-TOE / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL


Mass: 164.200 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H16O4
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 552 / 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: 2.68 Å3/Da / Density % sol: 54.03 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50-75 mM Potassium Maleate Buffer pH 7.0-8.0, 1 mM dithiothreitol, 38-46% Ammonium Sulfate, 1-3.5% PEG 1000 or PEG 1450, 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: Oct 4, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 74555 / Num. obs: 74518 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.7 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 8.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.1-2.145.70.7611100
2.14-2.185.70.6621100
2.18-2.225.70.5731100
2.22-2.265.70.5291100
2.26-2.315.70.4671100
2.31-2.375.60.4391100
2.37-2.425.70.3531100
2.42-2.495.70.3021100
2.49-2.565.70.2731100
2.56-2.655.70.2351100
2.65-2.745.70.1831100
2.74-2.855.70.1521100
2.85-2.985.70.1191100
2.98-3.145.70.0931100
3.14-3.335.70.0751100
3.33-3.595.70.0651100
3.59-3.955.70.0521100
3.95-4.525.70.0411100
4.52-5.75.60.0361100
5.7-505.40.032199.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PZX

3pzx
PDB Unreleased entry


Resolution: 2.1→40.92 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.915 / Occupancy max: 1 / Occupancy min: 0 / SU B: 11.172 / SU ML: 0.192 / SU R Cruickshank DPI: 0.1722 / Cross valid method: THROUGHOUT / ESU R: 0.251 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2739 3753 5 %RANDOM
Rwork0.23405 ---
obs0.23609 70764 99.89 %-
all-74585 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.792 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20.27 Å2-0 Å2
2--0.27 Å2-0 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8229 0 73 552 8854
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0198442
X-RAY DIFFRACTIONr_bond_other_d0.0010.028201
X-RAY DIFFRACTIONr_angle_refined_deg1.7471.98311460
X-RAY DIFFRACTIONr_angle_other_deg0.876318831
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.27651112
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.31324.375320
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.056151365
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8781545
X-RAY DIFFRACTIONr_chiral_restr0.0980.21348
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219579
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021774
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: 32860 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.102→2.157 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 273 -
Rwork0.34 5150 -
obs--99.21 %
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)
10.2857-0.10470.28560.2609-0.21070.3383-0.0826-0.12960.00330.02220.0805-0.0209-0.0553-0.1220.00210.48030.10090.0020.5246-0.00090.519-0.870958.8964-13.7473
20.21090.00940.05710.31060.02310.0661-0.0658-0.01420.0102-0.05470.0595-0.02060.0032-0.01230.00640.48470.0073-0.00910.4617-0.01160.55937.407561.3963-35.5398
30.2136-0.01970.35560.45470.25830.876-0.05960.04950.0278-0.03520.049-0.0682-0.136-0.08980.01070.47320.0780.00620.46880.03050.590611.90564.479-12.0872
40.2785-0.18640.35390.1956-0.21480.9822-0.2434-0.2160.05130.12150.1858-0.1941-0.2718-0.5460.05750.51180.2673-0.02650.7169-0.05630.4542-0.730162.261516.9119
55.1449-0.8928-1.58561.7036-0.28081.72-1.0853-0.7161-0.21541.18880.701-1.0831-0.5849-0.42880.38441.140.7672-0.68140.7913-0.45640.822310.752461.997131.1718
60.2448-0.18140.30990.1721-0.15350.6281-0.1171-0.3227-0.07010.19610.2845-0.0241-0.0159-0.4853-0.16750.46060.12440.00780.69880.06550.4651.474148.59499.3463
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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