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- PDB-7d4l: X-ray crystal Structure of E.coli Dihydrofolate Reductase complex... -

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Basic information

Entry
Database: PDB / ID: 7d4l
TitleX-ray crystal Structure of E.coli Dihydrofolate Reductase complexed with folate and NADP+ at pH7.0
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / dihydrofolate / reductase / alpha-beta sandiwitch / NADPH
Function / homology
Function and homology information


methotrexate binding / dihydrofolic acid binding / 10-formyltetrahydrofolate biosynthetic process / response to methotrexate / NADP+ binding / folic acid biosynthetic process / folic acid binding / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity ...methotrexate binding / dihydrofolic acid binding / 10-formyltetrahydrofolate biosynthetic process / response to methotrexate / NADP+ binding / folic acid biosynthetic process / folic acid 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 conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase-like domain superfamily
Similarity search - Domain/homology
FOLIC ACID / : / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
Model detailsX-ray diffraction
AuthorsWan, Q. / Dealwis, C.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32071264 China
National Science Foundation (NSF, China)31670790 China
CitationJournal: Acs Catalysis / Year: 2021
Title: Capturing the Catalytic Proton of Dihydrofolate Reductase: Implications for General Acid-Base Catalysis
Authors: Wan, Q. / Bennett, B.C. / Wymore, T. / Li, Z. / Wilson, M.A. / Brooks III, C.L. / Langan, P. / Kovalevsky, A. / Dealwis, C.G.
History
DepositionSep 24, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2604
Polymers18,0201
Non-polymers1,2403
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-3 kcal/mol
Surface area8020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.293, 45.625, 98.974
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Dihydrofolate reductase


Mass: 18020.326 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: folA, tmrA, b0048, JW0047 / Plasmid: pET-sumo / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ABQ4, dihydrofolate reductase
#2: Chemical ChemComp-FOL / FOLIC ACID


Mass: 441.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H19N7O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.15 Å3/Da / Density % sol: 42.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 40mg/mL DHFR-folate-NADP+ complex, 12% (v/v) PEG 400, 100mM MnCl2, 20mM imidazole, pH7.0

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Data collection

DiffractionMean temperature: 291 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 10, 2014 / Details: VariMax
RadiationMonochromator: CHOPPER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 20795 / % possible obs: 97.7 % / Redundancy: 4.1 % / Biso Wilson estimate: 18.08 Å2 / Rmerge(I) obs: 0.097 / Χ2: 1.081 / Net I/σ(I): 13.7
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 4 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 2.97 / Num. unique obs: 1017 / Χ2: 0.98 / % possible all: 94

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1rx2

1rx2


Resolution: 1.6→27.41 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1956 1068 5.15 %
Rwork0.1767 19683 -
obs0.1776 20751 97.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.28 Å2 / Biso mean: 21.0129 Å2 / Biso min: 9.6 Å2
Refinement stepCycle: final / Resolution: 1.6→27.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1268 0 81 87 1436
Biso mean--18.91 30.82 -
Num. residues----159
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6-1.670.23031420.2093231694
1.67-1.760.24551260.2044237496
1.76-1.870.19041390.1883239297
1.87-2.010.21951460.1757241097
2.01-2.220.23461350.1799244498
2.22-2.540.20791190.1895250899
2.54-3.20.22331390.19352538100

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