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- PDB-1vj3: STRUCTURAL STUDIES ON BIO-ACTIVE COMPOUNDS. CRYSTAL STRUCTURE AND... -

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Basic information

Entry
Database: PDB / ID: 1vj3
TitleSTRUCTURAL STUDIES ON BIO-ACTIVE COMPOUNDS. CRYSTAL STRUCTURE AND MOLECULAR MODELING STUDIES ON THE PNEUMOCYSTIS CARINII DIHYDROFOLATE REDUCTASE COFACTOR COMPLEX WITH TAB, A HIGHLY SELECTIVE ANTIFOLATE.
ComponentsDIHYDROFOLATE REDUCTASE
KeywordsOXIDOREDUCTASE / TAB / NADPH / MOLECULAR MODELING
Function / homology
Function and homology information


dihydrofolate metabolic 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-NDP / Chem-TAB / Dihydrofolate reductase
Similarity search - Component
Biological speciesPneumocystis carinii (fungus)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsCody, V. / Galitsky, N. / Rak, D. / Luft, J.R. / Queener, S.F. / Laughton, C.A. / Malcolm, F.G.
Citation
Journal: Biochemistry / Year: 2000
Title: Structural studies on bioactive compounds. 30. Crystal structure and molecular modeling studies on the Pneumocystis carinii dihydrofolate reductase cofactor complex with TAB, a highly selective antifolate.
Authors: Cody, V. / Chan, D. / Galitsky, N. / Rak, D. / Luft, J.R. / Pangborn, W. / Queener, S.F. / Laughton, C.A. / Stevens, M.F.
#1: Journal: Biochemistry / Year: 1999
Title: Ligand-Induced Conformational Changes in the Crystal Structures of Pneumocystis Carinii Dihydrofolate Reductase Complexes with Folate and Nadp+
Authors: Cody, V. / Galitsky, N. / Rak, D. / Luft, J.R. / Pangborn, W. / Queener, S.F.
#2: 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
DepositionJan 13, 2004Deposition site: RCSB / Processing site: RCSB
SupersessionJan 20, 2004ID: 1D8R
Revision 1.0Jan 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: 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)25,0013
Polymers23,7871
Non-polymers1,2132
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.481, 43.137, 61.288
Angle α, β, γ (deg.)90.00, 94.74, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO 71 OMEGA = 0.02
2: CIS GLYCINE - GLY 125 OMEGA = 0.07 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

#1: Protein DIHYDROFOLATE REDUCTASE


Mass: 23787.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pneumocystis carinii (fungus) / Gene: C-DNA P.CARINII DHFR / Plasmid: PT7-7 / 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-TAB / ACETIC ACID N-[2-CHLORO-5-[6-ETHYL-2,4-DIAMINO-PYRIMID-5-YL]-PHENYL]-[BENZYL-TRIAZEN-3-YL]ETHYL ESTER


Mass: 467.951 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H26ClN7O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.08 Å3/Da / Density % sol: 48 %
Crystal growpH: 6 / Details: pH 6.00
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
250 %(w/v)PEG200011
3100 mM11KCl
450 mMMES11pH6.0
1MES/KCl11

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 1, 1998
RadiationMonochromator: GRAPH / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→8 Å / Num. obs: 10325 / % possible obs: 97.8 % / Observed criterion σ(I): 1 / Redundancy: 2.2 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 4.1
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.187 / % possible all: 96.9
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 8 Å / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
% possible obs: 97.8 %

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Processing

Software
NameClassification
DENZOdata reduction
AMoREphasing
PROFFTrefinement
RefinementResolution: 2.1→8 Å / σ(F): 2
RfactorNum. reflection% reflection
obs0.19 10325 97.8 %
all-11328 -
Displacement parametersBiso mean: 24.34 Å2
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1678 0 94 75 1847
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.02
X-RAY DIFFRACTIONp_angle_d0.0650.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0810.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.5641.75
X-RAY DIFFRACTIONp_mcangle_it2.3782.5
X-RAY DIFFRACTIONp_scbond_it1.6411.75
X-RAY DIFFRACTIONp_scangle_it2.4262.5
X-RAY DIFFRACTIONp_plane_restr0.0160.02
X-RAY DIFFRACTIONp_chiral_restr0.2280.15
X-RAY DIFFRACTIONp_singtor_nbd0.2290.5
X-RAY DIFFRACTIONp_multtor_nbd0.3130.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.3340.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.43
X-RAY DIFFRACTIONp_staggered_tor23.615
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.1 Å / Rfactor obs: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS

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