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- PDB-1qzf: Crystal structure of DHFR-TS from Cryptosporidium hominis -

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Basic information

Entry
Database: PDB / ID: 1qzf
TitleCrystal structure of DHFR-TS from Cryptosporidium hominis
Componentsbifunctional dihydrofolate reductase-thymidylate synthase
KeywordsOXIDOREDUCTASE / TRANSFERASE / bifunctional enzyme
Function / homology
Function and homology information


thymidylate synthase activity / dTMP biosynthetic process / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / methylation / nucleotide binding
Similarity search - Function
Bifunctional dihydrofolate reductase/thymidylate synthase / Thymidylate Synthase; Chain A / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase ...Bifunctional dihydrofolate reductase/thymidylate synthase / Thymidylate Synthase; Chain A / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase / Thymidylate synthase, active site / Thymidylate synthase active site. / Thymidylate synthase / Thymidylate synthase/dCMP hydroxymethylase domain / Thymidylate synthase/dCMP hydroxymethylase superfamily / Thymidylate synthase / Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase-like domain superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
10-PROPARGYL-5,8-DIDEAZAFOLIC ACID / FOLIC ACID / Chem-NDP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Bifunctional dihydrofolate reductase-thymidylate synthase
Similarity search - Component
Biological speciesCryptosporidium hominis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsO'Neil, R.H. / Lilien, R.H. / Donald, B.R. / Stroud, R.M. / Anderson, A.C.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Phylogenetic classification of protozoa based on the structure of the linker domain in the bifunctional enzyme, dihydrofolate reductase-thymidylate synthase
Authors: O'Neil, R.H. / Lilien, R.H. / Donald, B.R. / Stroud, R.M. / Anderson, A.C.
History
DepositionSep 16, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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

Downloads & links

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Assembly

Deposited unit
A: bifunctional dihydrofolate reductase-thymidylate synthase
B: bifunctional dihydrofolate reductase-thymidylate synthase
C: bifunctional dihydrofolate reductase-thymidylate synthase
D: bifunctional dihydrofolate reductase-thymidylate synthase
E: bifunctional dihydrofolate reductase-thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)311,17525
Polymers301,3135
Non-polymers9,86220
Water7,314406
1
A: bifunctional dihydrofolate reductase-thymidylate synthase
B: bifunctional dihydrofolate reductase-thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,47010
Polymers120,5252
Non-polymers3,9458
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16220 Å2
ΔGint-47 kcal/mol
Surface area38350 Å2
MethodPISA
2
C: bifunctional dihydrofolate reductase-thymidylate synthase
D: bifunctional dihydrofolate reductase-thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,47010
Polymers120,5252
Non-polymers3,9458
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16250 Å2
ΔGint-47 kcal/mol
Surface area38330 Å2
MethodPISA
3
E: bifunctional dihydrofolate reductase-thymidylate synthase
hetero molecules

E: bifunctional dihydrofolate reductase-thymidylate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,47010
Polymers120,5252
Non-polymers3,9458
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_457-x-1,y,-z+21
Unit cell
Length a, b, c (Å)214.900, 116.300, 219.700
Angle α, β, γ (deg.)90.00, 95.23, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-609-

HOH

DetailsThe biological assembly is a dimer. Two dimers (chains A,B and C,D) are present in the asymmetric unit and another dimer is generated using the monomer, E, and the two-fold axis: -x,y,-z

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
bifunctional dihydrofolate reductase-thymidylate synthase


Mass: 60262.520 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium hominis (eukaryote) / Production host: Escherichia coli (E. coli) / Strain (production host): PA414
References: UniProt: Q27552, dihydrofolate reductase, thymidylate synthase

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Non-polymers , 5 types, 426 molecules

#2: Chemical
ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP / Deoxyuridine monophosphate


Mass: 308.182 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Chemical
ChemComp-CB3 / 10-PROPARGYL-5,8-DIDEAZAFOLIC ACID


Mass: 477.469 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C24H23N5O6
#4: Chemical
ChemComp-FOL / FOLIC ACID / Folate


Mass: 441.397 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C19H19N7O6
#5: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 4.54 Å3/Da / Density % sol: 72.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 6000, ammonium sulfate, lithium sulfate, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
17 mg/mlprotein1drop
210 %PEG60001reservoir
350 mMammonium sulfate1reservoir
4150 mMlithium sulfate1reservoir
5100 mMTris1reservoirpH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.08 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Apr 5, 1998
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 134842 / % possible obs: 87.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 8.7
Reflection shellResolution: 2.8→2.9 Å / % possible all: 52.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1f28 AND 1cd2

1f28

1cd2


Resolution: 2.8→29.8 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3828805.98 / Data cutoff high rms absF: 3828805.98 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 5618 5.1 %RANDOM
Rwork0.225 ---
all0.225 132822 --
obs0.225 111000 83.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 21.4533 Å2 / ksol: 0.324071 e/Å3
Displacement parametersBiso mean: 38.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.08 Å20 Å2-6.4 Å2
2--10.72 Å20 Å2
3----9.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.56 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21115 0 675 406 22196
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d2.23
X-RAY DIFFRACTIONc_mcbond_it0.911.5
X-RAY DIFFRACTIONc_mcangle_it1.62
X-RAY DIFFRACTIONc_scbond_it1.182
X-RAY DIFFRACTIONc_scangle_it1.882.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.37 582 4.9 %
Rwork0.349 11259 -
obs-11259 53.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2HCPLIGS_FOLNDPDUCB.PARAMHCPLIGS_FOLNDPDUCB.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.8 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.604
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.23

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