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- PDB-3hy4: Structure of human MTHFS with N5-iminium phosphate -

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Basic information

Entry
Database: PDB / ID: 3hy4
TitleStructure of human MTHFS with N5-iminium phosphate
Components5-formyltetrahydrofolate cyclo-ligase
KeywordsLIGASE / antifolate / cancer / N5-iminium phosphate / 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 / folic acid binding / tetrahydrofolate interconversion ...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 / folic acid binding / tetrahydrofolate interconversion / folic acid metabolic process / mitochondrial matrix / mitochondrion / ATP binding / metal ion binding / cytoplasm / cytosol
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
Chem-N5G / NICKEL (II) ION / PHOSPHATE ION / 5-formyltetrahydrofolate cyclo-ligase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.795 Å
AuthorsWu, D. / Li, Y. / Song, G. / Cheng, C. / 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 / 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

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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)24,0847
Polymers23,2901
Non-polymers7946
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.065, 144.583, 60.149
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#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: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P49914, 5-formyltetrahydrofolate cyclo-ligase

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Non-polymers , 5 types, 52 molecules

#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-N5G / N-({trans-4-[({(2R,4R,4aS,6S,8aS)-2-amino-4-hydroxy-5-[(phosphonooxy)methyl]decahydropteridin-6-yl}methyl)amino]cyclohexyl}carbonyl)-L-glutamic acid


Mass: 567.530 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H38N7O10P
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.24 Å3/Da / Density % sol: 45.17 %
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: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. all: 6105 / Num. obs: 6020 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.7→2.8 Å / % possible all: 99.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HXT

3hxt


Resolution: 2.795→19.32 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.771 / SU ML: 0.48 / σ(F): 1.35 / Phase error: 28.8 / Stereochemistry target values: ML
Details: THE LIGAND N5G IN THIS ENTRY IS N5-IMINIUM PHOSPHATE. HOWEVER, THERE IS SOME DISCREPANCY IN THE GEOMETRY. THE GEOMETRY FOR N5G IS SUGGESTED BY THE REFINEMENT. THE CO-ORDINATES FIT WELL IN ...Details: THE LIGAND N5G IN THIS ENTRY IS N5-IMINIUM PHOSPHATE. HOWEVER, THERE IS SOME DISCREPANCY IN THE GEOMETRY. THE GEOMETRY FOR N5G IS SUGGESTED BY THE REFINEMENT. THE CO-ORDINATES FIT WELL IN THE ELECTRON DENSITY MAP. THE MAP WAS GENERATED USING A DATASET COLLECTED AT 2.8 ANGSTROM RESOLUTION. THE DENSITY FOR THE LIGAND IS UNAMBIGUOUS AND THEREFORE THE GEOMETRIES ARE CORRECT AND ARE AS THEY WOULD BE IN A BIOLOGICAL MOLECULE, WHERE THE MICRO ENVIRONMENT HAS A PROFOUND INFLUENCE ON THE GEOMETRIES OF THE LIGAND.
RfactorNum. reflection% reflection
Rfree0.2997 242 4.46 %
Rwork0.2259 5184 -
obs0.2292 5426 99.18 %
all-6105 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.489 Å2 / ksol: 0.368 e/Å3
Displacement parametersBiso max: 63.63 Å2 / Biso mean: 31.023 Å2 / Biso min: 17.55 Å2
Baniso -1Baniso -2Baniso -3
1-5.886 Å20 Å2-0 Å2
2--1.458 Å20 Å2
3----7.345 Å2
Refinement stepCycle: LAST / Resolution: 2.795→19.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1553 0 42 46 1641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041617
X-RAY DIFFRACTIONf_angle_d0.7692167
X-RAY DIFFRACTIONf_chiral_restr0.046228
X-RAY DIFFRACTIONf_plane_restr0.005276
X-RAY DIFFRACTIONf_dihedral_angle_d18.413643
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2 / % reflection obs: 99 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.795-3.5180.3491170.2525402657
3.518-19.3210.2751250.21326442769

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