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- PDB-1df7: DIHYDROFOLATE REDUCTASE OF MYCOBACTERIUM TUBERCULOSIS COMPLEXED W... -

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Basic information

Entry
Database: PDB / ID: 1df7
TitleDIHYDROFOLATE REDUCTASE OF MYCOBACTERIUM TUBERCULOSIS COMPLEXED WITH NADPH AND METHOTREXATE
ComponentsDIHYDROFOLATE REDUCTASE
KeywordsOXIDOREDUCTASE / DIHYDROFOLATE REDUCTASE / STRUCTURE-BASED INHIBITOR DESIGN / FOLATEANALOGS / ROSSMANN FOLD / NICOTINAMIDE ADENINE DINUCLEOTIDE / METHOTREXATE / TUBERCULOSIS
Function / homology
Function and homology information


glycine biosynthetic process / NADP+ binding / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / cytosol
Similarity search - Function
Dihydrofolate reductase / Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
METHOTREXATE / Chem-NDP / Dihydrofolate reductase / Dihydrofolate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsLi, R. / Sirawaraporn, R. / Chitnumsub, P. / Sirawaraporn, W. / Wooden, J. / Athappilly, F. / Turley, S. / Hol, W.G.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Three-dimensional structure of M. tuberculosis dihydrofolate reductase reveals opportunities for the design of novel tuberculosis drugs.
Authors: Li, R. / Sirawaraporn, R. / Chitnumsub, P. / Sirawaraporn, W. / Wooden, J. / Athappilly, F. / Turley, S. / Hol, W.G.
#1: Journal: Biochemistry / Year: 1997
Title: Comparison of Two Independent Crystal Structures of Human Dihydrofolate Reductase Ternary Complexes Reduced with Nicotinamide Adenine Dinucleotide Phosphate and the Very Tight-Binding Inhibitor PT523
Authors: Cody, V. / Galitsky, N. / Luft, J.R. / Pangborn, W. / Rosowsky, A. / Blakley, R.L.
History
DepositionNov 17, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: DIHYDROFOLATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3258
Polymers17,6611
Non-polymers1,6647
Water3,513195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.510, 60.510, 58.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DIHYDROFOLATE REDUCTASE / DHFR


Mass: 17660.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium tuberculosis (bacteria)
References: UniProt: P0A546, UniProt: P9WNX1*PLUS, dihydrofolate reductase

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Non-polymers , 5 types, 202 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Chemical ChemComp-MTX / METHOTREXATE


Mass: 454.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22N8O5 / Comment: chemotherapy*YM
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 3.05 Å3/Da / Density % sol: 59.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 4.5
Details: AMMONIUM SULFATE, SODIUM ACETATE, GLYCEROL, NADPH, METHOTREXATE, POTASSIUM PHOSPHATE, DTT, POTASSIUM CHLORIDE, pH 4.5, VAPOR DIFFUSION, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein1drop
25 %glycerol1drop
310 mMNADPH1drop
41.5-2.2 Mammonium sulfate1reservoir
50.1 M1reservoirNaAc
60.1 mM1reservoirNaN3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0188
DetectorType: SBC-2 / Detector: CCD / Date: Sep 17, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0188 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 23394 / Num. obs: 109952 / % possible obs: 99.7 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 27
Reflection shellResolution: 1.7→1.78 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.263 / % possible all: 99.7
Reflection
*PLUS
Num. obs: 23394 / Num. measured all: 109952
Reflection shell
*PLUS
% possible obs: 99.7 %

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Processing

Software
NameClassification
SHARPphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.7→50 Å / σ(F): 1 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.246 2311 -RANDOM
Rwork0.187 ---
obs0.187 23394 90 %-
all-23394 --
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1244 0 110 195 1549
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.69
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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