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- PDB-1cd2: LIGAND INDUCED CONFORMATIONAL CHANGES IN THE CRYSTAL STRUCTURES O... -

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Basic information

Entry
Database: PDB / ID: 1cd2
TitleLIGAND INDUCED CONFORMATIONAL CHANGES IN THE CRYSTAL STRUCTURES OF PNEUMOCYSTIS CARINII DIHYDROFOLATE REDUCTASE COMPLEXES WITH FOLATE AND NADP+
ComponentsDIHYDROFOLATE REDUCTASE
KeywordsOXIDOREDUCTASE / ONE-CARBON METABOLISM
Function / homology
Function and homology information


glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding
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
FOLIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesPneumocystis carinii (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCody, V. / Galitsky, N. / Luft, J.R. / Pangborn, W. / Blakley, R.L. / Gangjee, A.
Citation
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.
#1: 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.
#2: Journal: J.Biol.Chem. / Year: 1995
Title: Methotrexate-resistant variants of human dihydrofolate reductase with substitutions of leucine 22. Kinetics, crystallography, and potential as selectable markers.
Authors: Lewis, W.S. / Cody, V. / Galitsky, N. / Luft, J.R. / Pangborn, W. / Chunduru, S.K. / Spencer, H.T. / Appleman, J.R. / Blakley, R.L.
#3: Journal: J.Biol.Chem. / Year: 1994
Title: Methotrexate-resistant variants of human dihydrofolate reductase. Effects of Phe31 substitutions.
Authors: Chunduru, S.K. / Cody, V. / Luft, J.R. / Pangborn, W. / Appleman, J.R. / Blakley, R.L.
#4: Journal: Anti-Cancer Drug Des. / Year: 1992
Title: Crystal structure determination at 2.3 A of recombinant human dihydrofolate reductase ternary complex with NADPH and methotrexate-gamma-tetrazole.
Authors: Cody, V. / Luft, J.R. / Ciszak, E. / Kalman, T.I. / Freisheim, J.H.
History
DepositionMar 5, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 6, 2000Provider: 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 1.4Nov 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.5Aug 9, 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

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Assembly

Deposited unit
A: DIHYDROFOLATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1033
Polymers23,9191
Non-polymers1,1852
Water1,33374
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.465, 43.131, 61.306
Angle α, β, γ (deg.)90.00, 94.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DIHYDROFOLATE REDUCTASE / / DHFR


Mass: 23918.537 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH NADP+ AND FOLATE / Source: (gene. exp.) Pneumocystis carinii (fungus) / 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-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-FOL / FOLIC ACID / Folate


Mass: 441.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H19N7O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.06 Å3/Da / Density % sol: 40.38 %
Crystal growpH: 6
Details: 10 ML PROTEIN, 1 MICROLITER 50MM MES, PH 6.5, 100MM KCL, 9 ML 50%(W/W)PEG 2K., pH 6.00
Crystal grow
*PLUS
pH: 6 / Method: unknown / Details: temperature gradient
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 %(w/v)PEG2000110.007ml
250 mMMES11
3100 mM11KCl
4protein110.010ml
5MES/KCl110.003ml

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Aug 15, 1994
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.94→8 Å / Num. obs: 10428 / % possible obs: 84.7 % / Observed criterion σ(I): 2 / Redundancy: 3.09 % / Rmerge(I) obs: 0.086
Reflection shellResolution: 2.18→2.2 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.052 / Mean I/σ(I) obs: 2.6 / Rsym value: 33.3 / % possible all: 90.3
Reflection
*PLUS
Highest resolution: 1.94 Å / Lowest resolution: 8 Å / % possible obs: 84.7 % / Observed criterion σ(I): 2 / Redundancy: 3.09 %
Reflection shell
*PLUS
Highest resolution: 2.18 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.6

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Processing

Software
NameClassification
PROLSQrefinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DYR

1dyr


Resolution: 2.2→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.198 --
obs-10428 96.1 %
Displacement parametersBiso mean: 23.78 Å2
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1686 0 80 74 1840
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0270.02
X-RAY DIFFRACTIONp_angle_d0.0660.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.070.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.061.5
X-RAY DIFFRACTIONp_mcangle_it1.5861.5
X-RAY DIFFRACTIONp_scbond_it0.9361
X-RAY DIFFRACTIONp_scangle_it1.5271.5
X-RAY DIFFRACTIONp_plane_restr0.0190.02
X-RAY DIFFRACTIONp_chiral_restr0.240.15
X-RAY DIFFRACTIONp_singtor_nbd0.2430.5
X-RAY DIFFRACTIONp_multtor_nbd0.2710.5
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.270.5
X-RAY DIFFRACTIONp_planar_tor3.13
X-RAY DIFFRACTIONp_staggered_tor21.315
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor21.620
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 8 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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