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- PDB-3d84: Structural Analysis of a Holo Enzyme Complex of Mouse Dihydrofola... -

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Basic information

Entry
Database: PDB / ID: 3d84
TitleStructural Analysis of a Holo Enzyme Complex of Mouse Dihydrofolate Reductase with NADPH and a Ternary Complex with the Potent and Selective Inhibitor 2.4-Diamino-6-(-2'-hydroxydibenz[b,f]azepin-5-yl)methylpteridine
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / mouse DHFR holo enzyme and ternary ligand complex / NADP / One-carbon metabolism
Function / homology
Function and homology information


Metabolism of folate and pterines / regulation of removal of superoxide radicals / dihydrofolic acid binding / tetrahydrobiopterin biosynthetic process / tetrahydrofolate metabolic process / sequence-specific mRNA binding / response to methotrexate / dihydrofolate metabolic process / tetrahydrofolate interconversion / axon regeneration ...Metabolism of folate and pterines / regulation of removal of superoxide radicals / dihydrofolic acid binding / tetrahydrobiopterin biosynthetic process / tetrahydrofolate metabolic process / sequence-specific mRNA binding / response to methotrexate / dihydrofolate metabolic process / tetrahydrofolate interconversion / axon regeneration / folic acid binding / folic acid metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / NADPH binding / tetrahydrofolate biosynthetic process / mRNA regulatory element binding translation repressor activity / response to nicotine / positive regulation of nitric-oxide synthase activity / NADP binding / mitochondrial inner membrane / mitochondrial matrix / mRNA binding / mitochondrion / nucleus / cytosol / cytoplasm
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 / Dihydrofolate reductase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCody, V.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Structural analysis of a holoenzyme complex of mouse dihydrofolate reductase with NADPH and a ternary complex with the potent and selective inhibitor 2,4-diamino-6-(2'-hydroxydibenz[b,f]azepin- ...Title: Structural analysis of a holoenzyme complex of mouse dihydrofolate reductase with NADPH and a ternary complex with the potent and selective inhibitor 2,4-diamino-6-(2'-hydroxydibenz[b,f]azepin-5-yl)methylpteridine.
Authors: Cody, V. / Pace, J. / Rosowsky, A.
History
DepositionMay 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 20, 2013Group: Non-polymer description
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Aug 30, 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
X: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4334
Polymers21,5041
Non-polymers9303
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.226, 61.172, 43.150
Angle α, β, γ (deg.)90.00, 118.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Dihydrofolate reductase /


Mass: 21503.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: jm105 / Gene: Dhfr / Plasmid: pPH70d / Production host: Escherichia coli (E. coli) / References: UniProt: P00375, dihydrofolate reductase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.23 Å3/Da / Density % sol: 44.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 10 mM Hepes, pH 7.4, 17 mM Na acetate, pH 6.5, 85 mM Tris HCl, 25% PEG 4K, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 3, 2004 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→38.01 Å / Num. all: 14934 / Num. obs: 13551 / % possible obs: 90.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 9.5 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.034 / Rsym value: 0.05 / Net I/σ(I): 0.033
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 14 % / Rmerge(I) obs: 0.076 / Mean I/σ(I) obs: 0.9 / Num. unique all: 750 / Rsym value: 0.495 / % possible all: 50.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2fzj

2fzj


Resolution: 1.9→23.83 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.432 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.193 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2289 684 5 %RANDOM
Rwork0.18684 ---
all0.21 13551 --
obs0.18902 12865 90.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refine analyzeLuzzati sigma a free: 0.018 Å
Refinement stepCycle: LAST / Resolution: 1.9→23.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1513 0 60 83 1656
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221620
X-RAY DIFFRACTIONr_bond_other_d0.0020.0216
X-RAY DIFFRACTIONr_angle_refined_deg2.0632.0282194
X-RAY DIFFRACTIONr_angle_other_deg1.15332
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4835187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.37424.24773
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.71915293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9531511
X-RAY DIFFRACTIONr_chiral_restr0.1390.2235
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021203
X-RAY DIFFRACTIONr_nbd_refined0.2180.2694
X-RAY DIFFRACTIONr_nbd_other0.270.221
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21061
X-RAY DIFFRACTIONr_nbtor_other0.1440.23
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.291
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.211
X-RAY DIFFRACTIONr_mcbond_it1.0961.5969
X-RAY DIFFRACTIONr_mcangle_it1.81421526
X-RAY DIFFRACTIONr_scbond_it2.7673757
X-RAY DIFFRACTIONr_scangle_it4.114.5668
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 28 -
Rwork0.253 502 -
obs--48.94 %

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