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- PDB-1daj: COMPARISON OF TERNARY COMPLEXES OF PNEUMOCYSTIS CARINII AND WILD ... -

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Basic information

Entry
Database: PDB / ID: 1daj
TitleCOMPARISON OF TERNARY COMPLEXES OF PNEUMOCYSTIS CARINII AND WILD TYPE HUMAN DIHYDROFOLATE REDUCTASE WITH COENZYME NADPH AND A NOVEL CLASSICAL ANTITUMOR FURO[2,3D]PYRIMIDINE ANTIFOLATE
ComponentsDIHYDROFOLATE REDUCTASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


dihydrofolate metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / mitochondrion / cytosol
Similarity search - Function
Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-MOT / Chem-NDP / Dihydrofolate reductase
Similarity search - Component
Biological speciesPneumocystis carinii (fungus)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsCody, V. / Galitsky, N. / Luft, J.R. / Pangborn, W. / Gangjee, A. / Devraj, R. / Queener, S.F. / Blakley, R.L.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Comparison of ternary complexes of Pneumocystis carinii and wild-type human dihydrofolate reductase with coenzyme NADPH and a novel classical antitumor furo[2,3-d]pyrimidine antifolate.
Authors: Cody, V. / Galitsky, N. / Luft, J.R. / Pangborn, W. / Gangjee, A. / Devraj, R. / Queener, S.F. / Blakley, R.L.
#1: Journal: Structure / Year: 1994
Title: The Structure of Pneumocystis Carinii Dihydrofolate Reductase to 1.9 A Resolution
Authors: Champness, J.N. / Achari, A. / Ballantine, S.P. / Bryant, P.K. / Delves, C.J. / Stammers, D.K.
History
DepositionJul 29, 1997Processing site: BNL
Revision 1.0Dec 24, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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: DIHYDROFOLATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1063
Polymers23,9191
Non-polymers1,1882
Water90150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.171, 43.094, 61.049
Angle α, β, γ (deg.)90.00, 94.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DIHYDROFOLATE REDUCTASE


Mass: 23918.537 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pneumocystis carinii (fungus) / Gene: C-DNA PNEUMOCYSTIS CARINII DHF / Plasmid: PT7-7 / Gene (production host): C-DNA PNEUMOCYSTIS CARINII DHFR / Production host: Escherichia coli (E. coli) / References: UniProt: P16184, dihydrofolate reductase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-MOT / N-[4-[(2,4-DIAMINOFURO[2,3D]PYRIMIDIN-5-YL)METHYL]METHYLAMINO]-BENZOYL]-L-GLUTAMATE


Mass: 442.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22N6O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.6 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13.6 mg/mlprotein1drop
210 %(w/v)PEG80001drop
30.1 Mimidazole-HCl1drop
41 mMdithiothreitol1drop
50.1 Mimidazole-HCl1reservoir
61 mMdithiothreitol1reservoir
710 %(w/v)PEG80001reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jul 14, 1994
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 5958 / % possible obs: 65.5 % / Observed criterion σ(I): 2 / Redundancy: 3.09 % / Rmerge(I) obs: 0.07

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Processing

Software
NameVersionClassification
PROFFTrefinement
R-AXISIIdata reduction
RefinementResolution: 2.3→8 Å /
RfactorNum. reflection
Rwork0.181 -
obs-5631
Displacement parametersBiso mean: 26.72 Å2
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1686 0 80 42 1808
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0380.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0330.045
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.3271.75
X-RAY DIFFRACTIONp_mcangle_it2.1122.5
X-RAY DIFFRACTIONp_scbond_it1.2121.75
X-RAY DIFFRACTIONp_scangle_it1.7682.5
X-RAY DIFFRACTIONp_plane_restr0.010.02
X-RAY DIFFRACTIONp_chiral_restr0.1360.15
X-RAY DIFFRACTIONp_singtor_nbd0.2130.5
X-RAY DIFFRACTIONp_multtor_nbd0.2840.5
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2730.5
X-RAY DIFFRACTIONp_planar_tor1.83
X-RAY DIFFRACTIONp_staggered_tor20.415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor27.315
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS

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