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- PDB-3d80: Structural Analysis of a Holo Enzyme Complex of Mouse Dihydrofola... -

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Basic information

Entry
Database: PDB / ID: 3d80
TitleStructural Analysis of a Holo Enzyme Complex of Mouse Dihydrofolate Reductase with NADPH and a Ternary Complex wtih the Potent and Selective Inhibitor 2,4-Diamino-6-(2'-hydroxydibenz[b,f]azepin-5-yl)methylpteridine
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / mouse holo enzyme ternary ligand complex dihydrofolate reductase / NADP / One-carbon metabolism
Function / homology
Function and homology information


folate reductase activity / Metabolism of folate and pterines / oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor / regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / tetrahydrofolate metabolic process / response to methotrexate / tetrahydrofolate interconversion / dihydrofolate reductase / dihydrofolate reductase activity ...folate reductase activity / Metabolism of folate and pterines / oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor / regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / tetrahydrofolate metabolic process / response to methotrexate / tetrahydrofolate interconversion / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / NADP binding / mRNA binding / mitochondrion / nucleus / cytosol / cytoplasm
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 / Chem-Q22 / Dihydrofolate reductase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 1.2Jun 12, 2013Group: Atomic model
Revision 1.3Aug 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
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9116
Polymers21,5041
Non-polymers1,4075
Water5,693316
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.482, 61.300, 43.589
Angle α, β, γ (deg.)90.00, 117.23, 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 / Fragment: mouse dihdyrofolate reductase
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


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-Q22 / (4aS)-5-[(2,4-diaminopteridin-6-yl)methyl]-4a,5-dihydro-2H-dibenzo[b,f]azepin-8-ol


Mass: 385.422 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H19N7O
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 2.29 Å3/Da / Density % sol: 46.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.15 M Tris, pH 8.3, 75 mM Na cacodylate, pH 6.5, 21% PEG 4K, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Nov 11, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→31.61 Å / Num. all: 38237 / Num. obs: 35455 / % possible obs: 98.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.06 / Net I/σ(I): 5.3
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 31.5 / Num. unique all: 2589 / Rsym value: 0.02 / % possible all: 15.2

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Processing

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

2fzj


Resolution: 1.4→31.61 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / SU B: 1.37 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.077 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23573 1851 5 %RANDOM
Rwork0.19882 ---
all0.22 35455 --
obs0.20072 35455 97.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.942 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati sigma a free: 0.011 Å
Refinement stepCycle: LAST / Resolution: 1.4→31.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1513 0 95 316 1924
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221724
X-RAY DIFFRACTIONr_angle_refined_deg1.6822.0482353
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6335207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9022475
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.21515309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5261512
X-RAY DIFFRACTIONr_chiral_restr0.3740.2251
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021298
X-RAY DIFFRACTIONr_nbd_refined0.210.2828
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21160
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2239
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.238
X-RAY DIFFRACTIONr_mcbond_it0.8311.51001
X-RAY DIFFRACTIONr_mcangle_it1.37521598
X-RAY DIFFRACTIONr_scbond_it1.9763855
X-RAY DIFFRACTIONr_scangle_it2.9634.5747
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 142 -
Rwork0.299 2578 -
obs--97.39 %

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