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- PDB-4m6j: Crystal structure of human dihydrofolate reductase (DHFR) bound t... -

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Basic information

Entry
Database: PDB / ID: 4m6j
TitleCrystal structure of human dihydrofolate reductase (DHFR) bound to NADPH
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / Rossmann Fold / NADPH binding / folate binding
Function / homology
Function and homology information


regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / sequence-specific mRNA binding / response to methotrexate / dihydrofolate metabolic process / axon regeneration / folic acid binding / G1/S-Specific Transcription ...regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / sequence-specific mRNA binding / response to methotrexate / dihydrofolate metabolic process / axon regeneration / folic acid binding / G1/S-Specific Transcription / folic acid metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / NADPH binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / tetrahydrofolate biosynthetic process / mRNA regulatory element binding translation repressor activity / positive regulation of nitric-oxide synthase activity / one-carbon metabolic process / NADP binding / negative regulation of translation / mRNA binding / mitochondrion / cytosol
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.201 Å
AuthorsBhabha, G. / Ekiert, D.C. / Wright, P.E. / Wilson, I.A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Divergent evolution of protein conformational dynamics in dihydrofolate reductase.
Authors: Bhabha, G. / Ekiert, D.C. / Jennewein, M. / Zmasek, C.M. / Tuttle, L.M. / Kroon, G. / Dyson, H.J. / Godzik, A. / Wilson, I.A. / Wright, P.E.
History
DepositionAug 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2013Group: Database references
Revision 1.2Nov 20, 2013Group: Database references
Revision 1.3Sep 20, 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)22,2262
Polymers21,4811
Non-polymers7451
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.958, 65.525, 152.251
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-459-

HOH

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Components

#1: Protein Dihydrofolate reductase /


Mass: 21480.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHFR / Plasmid: pET21A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/PDNAY / References: UniProt: P00374, 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.26 Å3/Da / Density % sol: 45.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 24% PEG6000, 100 mM Tris, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 5, 2009
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 59318 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Rsym value: 0.11 / Net I/σ(I): 14
Reflection shellResolution: 1.2→1.23 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2 / Rsym value: 0.54 / % possible all: 76.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DLS

1dls


Resolution: 1.201→33.486 Å / SU ML: 0.11 / σ(F): 1.34 / Phase error: 17.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1845 3008 5.08 %RANDOM
Rwork0.1627 ---
obs0.1639 59264 96.75 %-
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.6 Å2
Refinement stepCycle: LAST / Resolution: 1.201→33.486 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1491 0 48 195 1734
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091746
X-RAY DIFFRACTIONf_angle_d1.482397
X-RAY DIFFRACTIONf_dihedral_angle_d14.705711
X-RAY DIFFRACTIONf_chiral_restr0.086256
X-RAY DIFFRACTIONf_plane_restr0.007311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.201-1.22070.23941060.22972019X-RAY DIFFRACTION73
1.2207-1.24170.2466990.20972304X-RAY DIFFRACTION84
1.2417-1.26430.22541360.19792506X-RAY DIFFRACTION91
1.2643-1.28860.21761410.17372570X-RAY DIFFRACTION95
1.2886-1.31490.20481310.15712744X-RAY DIFFRACTION98
1.3149-1.34350.16621470.15342699X-RAY DIFFRACTION100
1.3435-1.37480.20561590.14432721X-RAY DIFFRACTION100
1.3748-1.40910.17771490.14132767X-RAY DIFFRACTION100
1.4091-1.44720.15511400.13382736X-RAY DIFFRACTION100
1.4472-1.48980.16961350.1312772X-RAY DIFFRACTION100
1.4898-1.53790.17471580.13042719X-RAY DIFFRACTION100
1.5379-1.59290.16541430.12452776X-RAY DIFFRACTION100
1.5929-1.65670.15861500.12922755X-RAY DIFFRACTION100
1.6567-1.73210.15791400.13522779X-RAY DIFFRACTION100
1.7321-1.82340.18811330.1362774X-RAY DIFFRACTION100
1.8234-1.93760.16391460.13582751X-RAY DIFFRACTION100
1.9376-2.08720.13331580.14212765X-RAY DIFFRACTION100
2.0872-2.29720.17741700.14662767X-RAY DIFFRACTION100
2.2972-2.62950.22131590.1672804X-RAY DIFFRACTION100
2.6295-3.31240.20821580.16872811X-RAY DIFFRACTION99
3.3124-33.49940.1791500.1962717X-RAY DIFFRACTION92

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