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- PDB-1dyr: THE STRUCTURE OF PNEUMOCYSTIS CARINII DIHYDROFOLATE REDUCTASE TO ... -

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Basic information

Entry
Database: PDB / ID: 1dyr
TitleTHE STRUCTURE OF PNEUMOCYSTIS CARINII DIHYDROFOLATE REDUCTASE TO 1.9 ANGSTROMS RESOLUTION
ComponentsDIHYDROFOLATE REDUCTASE
KeywordsOXIDOREDUCTASE / OXIDO-REDUCTASE
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
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
Chem-NDP / TRIMETHOPRIM / Dihydrofolate reductase
Similarity search - Component
Biological speciesPneumocystis carinii (fungus)
MethodX-RAY DIFFRACTION / Resolution: 1.86 Å
AuthorsChampness, J.N. / Achari, A. / Ballantine, S.P. / Bryant, P.K. / Delves, C.J. / Stammers, D.K.
Citation
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.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Preliminary Crystallographic Data for Pneumocystis Carinii Dihydrofolate Reductase
Authors: Stammers, D.K. / Delves, C. / Ballantine, S. / Jones, E.Y. / Stuart, D.I. / Achari, A. / Bryant, P.K. / Champness, J.N.
#2: Journal: Protein Expr.Purif. / Year: 1993
Title: Refolding of Recombinant Pneumocystis Carinii Dihydrofolate Reductase and Characterization of the Enzyme
Authors: Delves, C.J. / Ballantine, S.P. / Tansik, R.L. / Baccanari, D.P. / Stammers, D.K.
History
DepositionSep 14, 1994Processing site: BNL
Revision 1.0Oct 15, 1995Provider: 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 / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_keywords / 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_keywords.text / _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)24,9543
Polymers23,9191
Non-polymers1,0362
Water2,936163
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.900, 43.600, 37.600
Angle α, β, γ (deg.)90.00, 117.70, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO 71
2: GLY 124 - GLY 125 OMEGA = 1.21 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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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) / Description: RAT-DERIVED / Gene: C-DNA P.CARINII DHFR / Plasmid: PT7-7 / Gene (production host): C-DNA P.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-TOP / TRIMETHOPRIM


Mass: 290.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H18N4O3 / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.12 Å3/Da / Density % sol: 41.99 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6 / Method: vapor diffusion, sitting drop / Details: Stammers, D.K., (1993) J.Mol.Biol., 230, 679.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115-19 %(w/v)PEG34001reservoir
250 mMMES1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: SIEMENS / Date: Jun 24, 1992
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 15602 / % possible obs: 83 % / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Rmerge(I) obs: 0.05
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. measured all: 41714 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.91 Å / % possible obs: 39 % / Num. unique obs: 1193 / Mean I/σ(I) obs: 2.61

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Processing

Software
NameClassification
PROFFTrefinement
XENGENdata reduction
RefinementResolution: 1.86→10 Å /
RfactorNum. reflection
obs0.181 14605
Displacement parametersBiso mean: 23.08 Å2
Refinement stepCycle: LAST / Resolution: 1.86→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1678 0 69 163 1910
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.02
X-RAY DIFFRACTIONp_angle_d0.0330.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0420.045
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.3590.5
X-RAY DIFFRACTIONp_mcangle_it2.4132
X-RAY DIFFRACTIONp_scbond_it4.2722
X-RAY DIFFRACTIONp_scangle_it5.9164
X-RAY DIFFRACTIONp_plane_restr0.010.01
X-RAY DIFFRACTIONp_chiral_restr0.2150.01
X-RAY DIFFRACTIONp_singtor_nbd0.1910.15
X-RAY DIFFRACTIONp_multtor_nbd0.1840.15
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2150.15
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor6.42
X-RAY DIFFRACTIONp_staggered_tor20.910
X-RAY DIFFRACTIONp_orthonormal_tor23.910
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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