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- PDB-8uw0: Escherichia coli DHFR bound to NADP+ and folate, 17.2 MGy dose -

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Basic information

Entry
Database: PDB / ID: 8uw0
TitleEscherichia coli DHFR bound to NADP+ and folate, 17.2 MGy dose
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / pterin / hydride transfer
Function / homology
Function and homology information


dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / metal ion binding / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.93 Å
AuthorsSmith, N. / Horswill, A.R. / Wilson, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM139978 United States
CitationJournal: To Be Published
Title: X-ray-driven chemistry and conformational heterogeneity in atomic resolution crystal structures of bacterial dihydrofolate reductases
Authors: Smith, N. / Horswill, A.R. / Wilson, M.A.
History
DepositionNov 5, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release

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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)19,4727
Polymers18,0671
Non-polymers1,4056
Water6,593366
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.980, 44.848, 98.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Dihydrofolate reductase


Mass: 18067.338 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: folA / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3TR70
#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 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 2.07 Å3/Da / Density % sol: 40.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 17% PEG 400, 20 mM imidazole pH 7.0, 125 mM MnCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 1-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 7, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 0.93→33.12 Å / Num. obs: 99062 / % possible obs: 97.2 % / Redundancy: 5.3 % / Biso Wilson estimate: 7.8 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.05 / Net I/σ(I): 29.6
Reflection shellResolution: 0.93→0.96 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 8.1 / Num. unique obs: 9233 / CC1/2: 0.958 / Rrim(I) all: 0.208 / % possible all: 91.7

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.93→33.12 Å / SU ML: 0.0413 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 7.7763
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1152 3003 3.03 %
Rwork0.1004 96002 -
obs0.1008 99005 97.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.33 Å2
Refinement stepCycle: LAST / Resolution: 0.93→33.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1271 0 84 366 1721
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01191979
X-RAY DIFFRACTIONf_angle_d1.56422763
X-RAY DIFFRACTIONf_chiral_restr0.0974267
X-RAY DIFFRACTIONf_plane_restr0.0117373
X-RAY DIFFRACTIONf_dihedral_angle_d14.1733747
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.93-0.940.13171280.11823938X-RAY DIFFRACTION84.53
0.94-0.960.12561180.10034498X-RAY DIFFRACTION96.91
0.96-0.980.0961350.08864529X-RAY DIFFRACTION96.76
0.98-10.10661460.08524497X-RAY DIFFRACTION96.43
1-1.020.08641390.08264466X-RAY DIFFRACTION96.2
1.02-1.040.09971540.07774460X-RAY DIFFRACTION95.79
1.04-1.060.09221650.07294417X-RAY DIFFRACTION95.4
1.06-1.090.09171520.07144400X-RAY DIFFRACTION94.89
1.09-1.120.08041290.0694422X-RAY DIFFRACTION94.87
1.12-1.150.08351340.06944473X-RAY DIFFRACTION95.9
1.15-1.190.08521260.074585X-RAY DIFFRACTION97.92
1.19-1.230.07871190.07624675X-RAY DIFFRACTION98.93
1.23-1.280.09531480.08034653X-RAY DIFFRACTION99.21
1.28-1.340.09471570.08054647X-RAY DIFFRACTION99.44
1.34-1.410.09441600.08664687X-RAY DIFFRACTION99.41
1.41-1.50.10111570.08794672X-RAY DIFFRACTION99.73
1.5-1.610.10341390.09084749X-RAY DIFFRACTION99.92
1.61-1.780.1181590.10114721X-RAY DIFFRACTION99.98
1.78-2.030.10991420.10514777X-RAY DIFFRACTION100
2.03-2.560.131460.11954813X-RAY DIFFRACTION99.58
2.56-33.120.15361500.12724923X-RAY DIFFRACTION97.75

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