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- PDB-3nxo: Perferential Selection of Isomer Binding from Chiral Mixtures: Al... -

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Basic information

Entry
Database: PDB / ID: 3nxo
TitlePerferential Selection of Isomer Binding from Chiral Mixtures: Alternate Binding Modes Observed for the E- and Z-isomers of a Series of 5-Substituted 2,4-Diaminofuro[2,3-d]pyrimidines as Ternary Complexes with NADPH and Human Dihydrofolate Reductase
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / E-Z-isomers binding preferences
Function / homology
Function and homology information


regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / response to methotrexate / sequence-specific mRNA binding / folic acid binding / axon regeneration / dihydrofolate metabolic process / G1/S-Specific Transcription ...regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / response to methotrexate / sequence-specific mRNA binding / folic acid binding / axon regeneration / dihydrofolate metabolic process / G1/S-Specific Transcription / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / NADPH binding / tetrahydrofolate biosynthetic process / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / one-carbon metabolic process / mRNA regulatory element binding translation repressor activity / NADP binding / negative regulation of translation / mRNA binding / mitochondrion / cytosol
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-D2B / Chem-NDP / Dihydrofolate reductase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsCody, V.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Preferential selection of isomer binding from chiral mixtures: alternate binding modes observed for the E and Z isomers of a series of 5-substituted 2,4-diaminofuro[2,3-d]pyrimidines as ...Title: Preferential selection of isomer binding from chiral mixtures: alternate binding modes observed for the E and Z isomers of a series of 5-substituted 2,4-diaminofuro[2,3-d]pyrimidines as ternary complexes with NADPH and human dihydrofolate reductase.
Authors: Cody, V. / Piraino, J. / Pace, J. / Li, W. / Gangjee, A.
History
DepositionJul 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 6, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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)22,9288
Polymers21,3781
Non-polymers1,5507
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.150, 84.150, 77.968
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Dihydrofolate reductase


Mass: 21377.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHFR, DHFRP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P00374, dihydrofolate reductase
#2: Chemical ChemComp-D2B / 5-[(1Z)-2-(2-methoxyphenyl)-3-methylbut-1-en-1-yl]furo[2,3-d]pyrimidine-2,4-diamine


Mass: 324.377 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20N4O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.49 Å3/Da / Density % sol: 50.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: K2PO4 with 30% saturated ammonium sulfate with 3% v/v ethanol, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.975 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 6, 2008 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.35→26.6 Å / Num. all: 45729 / Num. obs: 45197 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.7 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.025 / Net I/σ(I): 18.9
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 4.4 / Num. unique all: 6605 / Rsym value: 0.17 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0088refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1u70.pdb

1u70


Resolution: 1.35→26.62 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.956 / SU B: 0.822 / SU ML: 0.035 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20892 2276 5 %RANDOM
Rwork0.19132 ---
all0.1967 45197 --
obs0.19223 42917 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.678 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refine analyzeLuzzati coordinate error obs: 0.16 Å
Refinement stepCycle: LAST / Resolution: 1.35→26.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1504 0 97 165 1766
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0340.0221686
X-RAY DIFFRACTIONr_angle_refined_deg2.7882.0492301
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0715197
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.88824.93273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.45415296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.495158
X-RAY DIFFRACTIONr_chiral_restr0.1760.2241
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0211267
X-RAY DIFFRACTIONr_mcbond_it1.4921.5965
X-RAY DIFFRACTIONr_mcangle_it2.49121576
X-RAY DIFFRACTIONr_scbond_it3.6183721
X-RAY DIFFRACTIONr_scangle_it5.2974.5725
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 176 -
Rwork0.292 3163 -
obs-6605 100 %

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