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- PDB-5uio: structure of DHFR with bound DAP, p-ABG and NADP -

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Basic information

Entry
Database: PDB / ID: 5uio
Titlestructure of DHFR with bound DAP, p-ABG and NADP
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / DHFR / NADP / 2 / 4 diaminopyridine / N-(4aminobenzoyl)-L-glutamate
Function / homology
Function and homology information


methotrexate binding / dihydrofolic acid binding / 10-formyltetrahydrofolate biosynthetic process / response to methotrexate / folic acid biosynthetic process / folic acid binding / NADP+ binding / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity ...methotrexate binding / dihydrofolic acid binding / 10-formyltetrahydrofolate biosynthetic process / response to methotrexate / folic acid biosynthetic process / folic acid binding / NADP+ binding / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / NADPH binding / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / response to xenobiotic stimulus / response to antibiotic / 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
N-(4-aminobenzene-1-carbonyl)-L-glutamic acid / BETA-MERCAPTOETHANOL / FORMIC ACID / PYRIMIDINE-2,4-DIAMINE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.929 Å
AuthorsPedersen, L.C. / London, R.E.
CitationJournal: Biochemistry / Year: 2017
Title: A Structural Basis for Biguanide Activity.
Authors: Gabel, S.A. / Duff, M.R. / Pedersen, L.C. / DeRose, E.F. / Krahn, J.M. / Howell, E.E. / London, R.E.
History
DepositionJan 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydrofolate reductase
B: Dihydrofolate reductase
C: Dihydrofolate reductase
D: Dihydrofolate reductase
E: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,03224
Polymers96,0385
Non-polymers4,99419
Water11,097616
1
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3274
Polymers19,2081
Non-polymers1,1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4424
Polymers19,2081
Non-polymers2343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4526
Polymers19,2081
Non-polymers1,2445
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4065
Polymers19,2081
Non-polymers1,1984
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4065
Polymers19,2081
Non-polymers1,1984
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.781, 103.945, 145.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
Dihydrofolate reductase


Mass: 19207.625 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: folA / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABQ4, dihydrofolate reductase

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Non-polymers , 6 types, 635 molecules

#2: Chemical
ChemComp-LG3 / PYRIMIDINE-2,4-DIAMINE


Mass: 110.117 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H6N4
#3: Chemical
ChemComp-8DM / N-(4-aminobenzene-1-carbonyl)-L-glutamic acid


Mass: 266.250 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H14N2O5
#4: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#5: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS
#6: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 616 / 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: 2.47 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2mM NADP,10mM DAP,50mM p-ABP,0.2M Magnesium Formate,20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. obs: 72439 / % possible obs: 100 % / Redundancy: 7.9 % / Rsym value: 0.058 / Net I/σ(I): 18.6
Reflection shellResolution: 1.93→1.96 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 3616 / Rsym value: 0.475 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RA3

1ra3


Resolution: 1.929→35.446 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2304 1993 2.76 %
Rwork0.1915 --
obs0.1926 72115 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.929→35.446 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6312 0 317 616 7245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096889
X-RAY DIFFRACTIONf_angle_d0.8919403
X-RAY DIFFRACTIONf_dihedral_angle_d14.822439
X-RAY DIFFRACTIONf_chiral_restr0.052992
X-RAY DIFFRACTIONf_plane_restr0.0051199
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9287-1.97690.31061380.26994881X-RAY DIFFRACTION98
1.9769-2.03040.27621430.22064997X-RAY DIFFRACTION100
2.0304-2.09010.27281410.224971X-RAY DIFFRACTION100
2.0901-2.15760.2571400.21664935X-RAY DIFFRACTION100
2.1576-2.23470.27491430.20664999X-RAY DIFFRACTION100
2.2347-2.32420.25181420.20964983X-RAY DIFFRACTION100
2.3242-2.42990.25171410.2164998X-RAY DIFFRACTION100
2.4299-2.5580.27741420.21584964X-RAY DIFFRACTION100
2.558-2.71820.26281400.21644973X-RAY DIFFRACTION99
2.7182-2.9280.24911420.22344948X-RAY DIFFRACTION98
2.928-3.22240.26061400.21084975X-RAY DIFFRACTION99
3.2224-3.68830.20491450.17355096X-RAY DIFFRACTION100
3.6883-4.64520.18731440.15395092X-RAY DIFFRACTION100
4.6452-35.45170.19571520.16895310X-RAY DIFFRACTION100

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