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- PDB-7d3z: X-ray crystal Structure of E.coli Dihydrofolate Reductase complex... -

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Basic information

Entry
Database: PDB / ID: 7d3z
TitleX-ray crystal Structure of E.coli Dihydrofolate Reductase complexed with folate and NADP+ at pH4.5
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / dihydrofolate / reductase / alpha-beta sandiwitch / NADPH
Function / homology
Function and homology information


methotrexate binding / dihydrofolic acid binding / response to methotrexate / dihydrofolate metabolic process / NADP+ binding / folic acid binding / folic acid metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity ...methotrexate binding / dihydrofolic acid binding / response to methotrexate / dihydrofolate metabolic process / NADP+ binding / folic acid binding / folic acid metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / 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 domain / Dihydrofolate reductase / Dihydrofolate reductase (DHFR) domain profile. / 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: 1.65 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.
History
DepositionSep 21, 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

Downloads & links

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Assembly

Deposited unit
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2053
Polymers18,0201
Non-polymers1,1852
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint1 kcal/mol
Surface area7930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.102, 45.595, 99.113
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 / Folate


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 / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.14 Å3/Da / Density % sol: 42.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 40mg/mL DHFR-folate-NADP+ complex, 12% (v/v) PEG 400, 100mM MnCl2, 100mM NaAc, pH4.5

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Data collection

DiffractionMean temperature: 291 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.502 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 10, 2014
RadiationMonochromator: CHOPPER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.502 Å / Relative weight: 1
ReflectionResolution: 1.65→27.31 Å / Num. obs: 17684 / % possible obs: 91.74 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.04 / Χ2: 0.96 / Net I/σ(I): 25.3
Reflection shellResolution: 1.651→1.71 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.422 / Num. unique obs: 1108 / Χ2: 0.88 / % possible all: 58.07

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Processing

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

1rx2


Resolution: 1.65→27.31 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 16.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1816 904 5.11 %
Rwork0.1522 16778 -
obs0.1537 17682 91.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.8 Å2 / Biso mean: 17.4226 Å2 / Biso min: 3.98 Å2
Refinement stepCycle: final / Resolution: 1.65→27.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1268 0 80 120 1468
Biso mean--14.28 32.97 -
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 (%)
1.65-1.750.25611160.2185211471
1.75-1.890.19981580.1598280994
1.89-2.080.19921830.1512287797
2.08-2.380.20071410.1524295497
2.38-30.20421650.1599296297
Refinement TLS params.Method: refined / Origin x: 27.4868 Å / Origin y: 43.9763 Å / Origin z: 13.4397 Å
111213212223313233
T0.0441 Å2-0.0073 Å2-0.0036 Å2-0.0579 Å2-0.0012 Å2--0.0401 Å2
L1.1724 °2-0.4124 °20.0737 °2-1.3404 °2-0.3621 °2--1.0582 °2
S-0.0032 Å °-0.0828 Å °-0.0259 Å °0.0106 Å °0.0059 Å °-0.0658 Å °-0.0153 Å °0.0407 Å °-0.0057 Å °
Refinement TLS groupSelection details: (chain A and resseq 1:159)

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