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- PDB-3hy6: Structure of human MTHFS with ADP -

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Basic information

Entry
Database: PDB / ID: 3hy6
TitleStructure of human MTHFS with ADP
Components5-formyltetrahydrofolate cyclo-ligase
KeywordsLIGASE / antifolate / cancer / ADP / ATP-binding / Folate-binding / Magnesium / Nucleotide-binding
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
ADENOSINE-5'-DIPHOSPHATE / NICKEL (II) ION / PHOSPHATE ION / 5-formyltetrahydrofolate cyclo-ligase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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: Derived calculations / 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)24,28018
Polymers23,2901
Non-polymers99017
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: 5-formyltetrahydrofolate cyclo-ligase
hetero molecules

A: 5-formyltetrahydrofolate cyclo-ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,55936
Polymers46,5792
Non-polymers1,98034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area5110 Å2
ΔGint-284 kcal/mol
Surface area19160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.511, 145.221, 59.655
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-240-

HOH

21A-332-

HOH

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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, 164 molecules

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


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


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.26 Å3/Da / Density % sol: 45.47 %
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: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→72.55 Å / Num. all: 12640 / Num. obs: 12552 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2→2.1 Å / % possible all: 99.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.4.0066refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HXT

3hxt


Resolution: 2.1→46.09 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.933 / SU B: 6.42 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.278 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25527 610 4.9 %RANDOM
Rwork0.21535 ---
obs0.21728 11929 99.22 %-
all-12640 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.977 Å2
Baniso -1Baniso -2Baniso -3
1-1.36 Å20 Å20 Å2
2--0.71 Å20 Å2
3----2.06 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1579 0 29 147 1755
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221628
X-RAY DIFFRACTIONr_angle_refined_deg1.281.9872187
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4055199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.11823.55376
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.08915310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9331515
X-RAY DIFFRACTIONr_chiral_restr0.080.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211210
X-RAY DIFFRACTIONr_mcbond_it0.751.5993
X-RAY DIFFRACTIONr_mcangle_it1.4421591
X-RAY DIFFRACTIONr_scbond_it2.2733635
X-RAY DIFFRACTIONr_scangle_it3.8464.5596
LS refinement shellResolution: 2.104→2.159 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 33 -
Rwork0.286 812 -
obs--92.65 %

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