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- PDB-8vz4: L54G Mutant of E. coli Dihydrofolate Reductase Complexed with Nic... -

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Basic information

Entry
Database: PDB / ID: 8vz4
TitleL54G Mutant of E. coli Dihydrofolate Reductase Complexed with Nicotinamide Adenine Dinucleotide Phosphate (oxidized form)
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / L54G / NADP+ / DHFR
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 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsFried, S.D.E. / Boxer, S.G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1915727 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118044 United States
CitationJournal: To Be Published
Title: Role of Electrostatics in Hydride Transfer by Dihydrofolate Reductase
Authors: Fried, S.D.E. / Mukherjee, S. / Mao, Y. / Boxer, S.G.
History
DepositionFeb 9, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydrofolate reductase
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4134
Polymers35,9262
Non-polymers1,4872
Water6,431357
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.493, 58.592, 70.208
Angle α, β, γ (deg.)90.00, 102.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Dihydrofolate reductase


Mass: 17963.234 Da / Num. of mol.: 2 / Mutation: L54G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: folA, tmrA, b0048, JW0047 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ABQ4, dihydrofolate reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 42.92 % / Description: Rods
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG 6000, calcium chloride, Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.25→37.64 Å / Num. obs: 83315 / % possible obs: 98.5 % / Redundancy: 13.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.038 / Rrim(I) all: 0.144 / Χ2: 0.87 / Net I/σ(I): 10.1 / Num. measured all: 1134224
Reflection shellResolution: 1.25→1.27 Å / % possible obs: 91.4 % / Redundancy: 11.2 % / Rmerge(I) obs: 3.157 / Num. measured all: 42599 / Num. unique obs: 3797 / CC1/2: 0.762 / Rpim(I) all: 0.955 / Rrim(I) all: 3.305 / Χ2: 0.8 / Net I/σ(I) obs: 1.2

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→37.64 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1952 4118 4.97 %
Rwork0.1639 --
obs0.1654 82881 97.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.25→37.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2480 0 96 357 2933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142979
X-RAY DIFFRACTIONf_angle_d1.5794107
X-RAY DIFFRACTIONf_dihedral_angle_d20.6961165
X-RAY DIFFRACTIONf_chiral_restr0.111436
X-RAY DIFFRACTIONf_plane_restr0.014533
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.260.43231130.32212319X-RAY DIFFRACTION85
1.26-1.280.24721390.27742750X-RAY DIFFRACTION98
1.28-1.30.30381420.25452686X-RAY DIFFRACTION98
1.3-1.310.26861440.23282725X-RAY DIFFRACTION99
1.31-1.330.25811510.22212717X-RAY DIFFRACTION99
1.33-1.350.26541440.2232726X-RAY DIFFRACTION99
1.35-1.370.26981340.20972719X-RAY DIFFRACTION98
1.37-1.390.26351560.20052678X-RAY DIFFRACTION98
1.39-1.410.25741470.19392701X-RAY DIFFRACTION98
1.41-1.440.22641500.1912729X-RAY DIFFRACTION98
1.44-1.460.23521280.17972743X-RAY DIFFRACTION98
1.46-1.490.23311400.16862696X-RAY DIFFRACTION98
1.49-1.520.23571450.16432676X-RAY DIFFRACTION97
1.52-1.560.21471440.15292729X-RAY DIFFRACTION99
1.56-1.590.211430.14262724X-RAY DIFFRACTION99
1.59-1.630.21171380.14372756X-RAY DIFFRACTION99
1.63-1.680.19471520.1462743X-RAY DIFFRACTION99
1.68-1.730.20021350.14822732X-RAY DIFFRACTION99
1.73-1.780.17351470.14192717X-RAY DIFFRACTION99
1.78-1.840.19281430.14642739X-RAY DIFFRACTION98
1.84-1.920.20191330.14592691X-RAY DIFFRACTION98
1.92-2.010.18441380.14522742X-RAY DIFFRACTION98
2.01-2.110.15821340.14512680X-RAY DIFFRACTION96
2.11-2.240.17071550.13932756X-RAY DIFFRACTION100
2.24-2.420.18011390.15242810X-RAY DIFFRACTION100
2.42-2.660.21411530.16872741X-RAY DIFFRACTION100
2.66-3.040.19541420.17312802X-RAY DIFFRACTION100
3.04-3.830.15931370.15442733X-RAY DIFFRACTION97
3.84-37.640.1621520.15662803X-RAY DIFFRACTION98

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