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- PDB-3hxt: Structure of human MTHFS -

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Basic information

Entry
Database: PDB / ID: 3hxt
TitleStructure of human MTHFS
Components5-formyltetrahydrofolate cyclo-ligase
KeywordsLIGASE / antifolate / cancer / one-carbon metabolic network / Acetylation / ATP-binding / Cytoplasm / Folate-binding / Magnesium / Nucleotide-binding / Polymorphism
Function / homology
Function and homology information


folic acid catabolic process / 5-formyltetrahydrofolate cyclo-ligase / 5-formyltetrahydrofolate cyclo-ligase activity / folic acid-containing compound biosynthetic process / formate metabolic process / glutamate metabolic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / folic acid binding ...folic acid catabolic process / 5-formyltetrahydrofolate cyclo-ligase / 5-formyltetrahydrofolate cyclo-ligase activity / folic acid-containing compound biosynthetic process / formate metabolic process / glutamate metabolic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / folic acid binding / folic acid metabolic process / mitochondrial matrix / mitochondrion / ATP binding / metal ion binding / cytosol / cytoplasm
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
NICKEL (II) ION / 5-formyltetrahydrofolate cyclo-ligase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWu, D. / Li, Y. / Song, G. / Cheng, C. / Zhang, R. / Joachimiak, A. / Shaw, N. / Liu, Z.-J.
CitationJournal: Cancer Res. / Year: 2009
Title: Structural basis for the inhibition of human 5,10-methenyltetrahydrofolate synthetase by N10-substituted folate analogues
Authors: Wu, D. / Li, Y. / Song, G. / Cheng, C. / Zhang, R. / Joachimiak, A. / Shaw, N. / Liu, Z.-J.
History
DepositionJun 22, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5-formyltetrahydrofolate cyclo-ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,69512
Polymers23,2901
Non-polymers40511
Water2,810156
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.705, 145.122, 59.218
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-212-

MG

21A-243-

HOH

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Components

#1: Protein 5-formyltetrahydrofolate cyclo-ligase / / 5 / 10-methenyl-tetrahydrofolate synthetase / Methenyl-THF synthetase / MTHFS


Mass: 23289.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MTHFS / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P49914, 5-formyltetrahydrofolate cyclo-ligase
#2: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.25 Å3/Da / Density % sol: 45.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 100mM HEPES, pH6.6, 20mM MgCl2.6H2O, 20mM NiCl2.6H2O, 20% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 17011 / Num. obs: 17011 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.9→1.93 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
BALBESphasing
REFMAC5.4.0066refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1U3G

1u3g


Resolution: 1.9→30.94 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / SU B: 7.251 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.429 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25019 859 5.1 %RANDOM
Rwork0.21008 ---
obs0.212 16137 98.88 %-
all-17011 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.33 Å2
Baniso -1Baniso -2Baniso -3
1-1.98 Å20 Å20 Å2
2---0.33 Å20 Å2
3----1.66 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1557 0 11 156 1724
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221574
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.141.9782109
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2255191
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.28523.46775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.89415302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4731515
X-RAY DIFFRACTIONr_chiral_restr0.0780.2227
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211174
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_it1.2891.5962
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.44821540
X-RAY DIFFRACTIONr_scbond_it2.7193612
X-RAY DIFFRACTIONr_scangle_it4.7194.5569
X-RAY DIFFRACTIONr_rigid_bond_restr1.67431570
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded6.9531546
LS refinement shellResolution: 1.893→1.942 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 52 -
Rwork0.306 1050 -
obs--86.57 %
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)
19.89625.6822.39628.02592.73225.0135-0.11930.2004-0.3264-0.19750.0993-0.19020.1595-0.09440.020.11930.03720.00360.1240.01110.098533.828152.7053-7.6406
217.01486.98551.88277.29746.00716.39330.12270.7433-0.1645-0.4856-0.0714-0.850.22080.9404-0.05140.15320.00820.01480.1451-0.0020.132623.574142.5207-8.2499
31.2217-2.3426-2.7934.89216.738111.1609-0.01220.1822-0.1939-0.0415-0.09670.12110.2213-0.20960.10890.0981-0.0108-0.00630.10750.01770.127810.393538.61920.7894
42.4227-0.674-0.74042.1255-0.04662.407-0.02370.0294-0.16930.049-0.01830.06280.1795-0.1380.0420.0469-0.0143-0.01240.0510.00450.07235.688751.77054.6657
59.35581.3654-2.42285.9902-0.43476.1152-0.010.39540.1357-0.36080.0423-0.3507-0.10710.2167-0.03230.1030.0188-0.04150.0619-0.00710.077511.006264.3358-6.0247
66.69581.8439-2.29192.9375-1.57114.5144-0.1172-0.0937-0.15110.01770.05560.00050.10960.05810.06170.10040.0013-0.0310.0536-0.0060.07852.536455.4557-9.1949
73.0518-1.16942.11582.60110.70833.1956-0.10350.05280.1839-0.09250.0220.0917-0.3837-0.15350.08160.0637-0.03150.02740.08720.00820.11555.514665.3663-0.2092
84.8680.554-1.82722.70951.35781.6122-0.03350.06760.09-0.00160.0208-0.2556-0.07880.14590.01260.1138-0.00770.0010.0913-0.01450.113522.456351.9590.3384
92.01110.78981.1523.17581.39446.47440.0064-0.29730.18980.20970.1273-0.2938-0.14550.4787-0.13360.08190.0001-0.0020.09370.01440.121616.9165.84825.4388
101.1494-0.17740.17511.51060.38130.8055-0.04090.053-0.14930.05920.0443-0.11310.20910.1658-0.00330.085-0.00610.00170.08470.01350.073319.582746.71553.7658
114.1285-0.6832-1.17821.1191.08473.83330.05670.00170.0413-0.1139-0.0371-0.3114-0.11470.2189-0.01960.11550.0313-0.03410.12750.01240.09523.922949.16085.6306
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 16
2X-RAY DIFFRACTION2A17 - 21
3X-RAY DIFFRACTION3A24 - 41
4X-RAY DIFFRACTION4A42 - 80
5X-RAY DIFFRACTION5A81 - 95
6X-RAY DIFFRACTION6A96 - 112
7X-RAY DIFFRACTION7A113 - 132
8X-RAY DIFFRACTION8A133 - 151
9X-RAY DIFFRACTION9A152 - 167
10X-RAY DIFFRACTION10A168 - 181
11X-RAY DIFFRACTION11A182 - 199

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