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- PDB-2cd2: LIGAND INDUCED CONFORMATIONAL CHANGES IN THE CRYSTAL STRUCTURES O... -

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Basic information

Entry
Database: PDB / ID: 2cd2
TitleLIGAND INDUCED CONFORMATIONAL CHANGES IN THE CRYSTAL STRUCTURES OF PNEUMOCYSTIS CARINII DIHYDROFOLATE REDUCTASE COMPLEXES WITH FOLATE AND NADP+
ComponentsDIHYDROFOLATE REDUCTASE
KeywordsOXIDOREDUCTASE / OXIDO-REDUCTASE / FOLATE / NADPH
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
FOLIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesPneumocystis carinii (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCody, V. / Galitsky, N. / Rak, D. / Luft, J. / Pangborn, W. / Queener, S.
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: Structure (London) / Year: 1994
Title: THE STRUCTURE OF PNEUMOCYSTIS CARINII DIHYDROFOLATE REDUCTASE TO 1.9 ANGSTROMS RESOLUTION
Authors: CHAMPNESS, J.N. / ACHARI, A. / BALLANTINE, S.P. / BRYANT, P.K. / DELVES, C.J. / STAMMERS, D.K.
History
DepositionMar 15, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 29, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
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

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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
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.305, 43.145, 61.147
Angle α, β, γ (deg.)90.00, 94.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DIHYDROFOLATE REDUCTASE / PCDHFR


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) / Variant: BACTERIA / 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


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


Mass: 441.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H19N7O6
#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: 1.97 Å3/Da / Density % sol: 48 %
Crystal growpH: 6 / Details: pH 6.00
Crystal
*PLUS
Density % sol: 48 %
Crystal grow
*PLUS
pH: 6 / Method: unknown / Details: temperature gradient
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
350 %(w/v)PEG2000110.007ml
450 mMMES11
5100 mM11KCl
1protein110.010ml
2MES/KCl110.003ml

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorDate: Mar 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→8 Å / Num. obs: 15078 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 12.8
Reflection shellResolution: 1.9→8 Å
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 8 Å / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 2.6 %
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 8 Å

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Processing

Software
NameClassification
PROLSQrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.196 --
obs-12871 97.4 %
Displacement parametersBiso mean: 29.35 Å2
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1686 0 80 75 1841
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0410.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0450.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.6411.75
X-RAY DIFFRACTIONp_mcangle_it2.7052.5
X-RAY DIFFRACTIONp_scbond_it2.8982.5
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0110.02
X-RAY DIFFRACTIONp_chiral_restr0.170.15
X-RAY DIFFRACTIONp_singtor_nbd0.1920.5
X-RAY DIFFRACTIONp_multtor_nbd0.2510.5
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2240.5
X-RAY DIFFRACTIONp_planar_tor2.13
X-RAY DIFFRACTIONp_staggered_tor20.115
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor18.715
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 8 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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