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- PDB-9ni0: L54A Mutant of E. coli Dihydrofolate Reductase Complexed with Nic... -

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Basic information

Entry
Database: PDB / ID: 9ni0
TitleL54A Mutant of E. coli Dihydrofolate Reductase Complexed with Nicotinamide Adenine Dinucleotide Phosphate (oxidized form)
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / L54A / NADP+ / DHFR
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 / 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: 1.51 Å
AuthorsFried, S.D.E. / Boxer, S.G.
Funding support United States, 1items
OrganizationGrant numberCountry
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 25, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2025Provider: 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
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5216
Polymers35,9552
Non-polymers1,5674
Water3,819212
1
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7613
Polymers17,9771
Non-polymers7832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7613
Polymers17,9771
Non-polymers7832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.597, 58.812, 71.276
Angle α, β, γ (deg.)90.00, 102.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Dihydrofolate reductase


Mass: 17977.260 Da / Num. of mol.: 2 / Mutation: L54A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: folA, c0058 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ABQ5, 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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.2 Å3/Da / Density % sol: 44.03 % / 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 31, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.51→37.7 Å / Num. obs: 48391 / % possible obs: 98.6 % / Redundancy: 7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.04 / Rrim(I) all: 0.106 / Χ2: 0.73 / Net I/σ(I): 9.2 / Num. measured all: 337513
Reflection shellResolution: 1.51→1.53 Å / % possible obs: 93.9 % / Redundancy: 5.9 % / Rmerge(I) obs: 1.401 / Num. measured all: 13467 / Num. unique obs: 2267 / CC1/2: 0.741 / Rpim(I) all: 0.61 / Rrim(I) all: 1.534 / Χ2: 0.62 / Net I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→37.7 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.221 2424 5.03 %
Rwork0.198 --
obs0.2 48148 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.51→37.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2454 0 98 212 2764
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072922
X-RAY DIFFRACTIONf_angle_d1.3184042
X-RAY DIFFRACTIONf_dihedral_angle_d27.168473
X-RAY DIFFRACTIONf_chiral_restr0.075432
X-RAY DIFFRACTIONf_plane_restr0.008505
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.540.31891350.31772534X-RAY DIFFRACTION92
1.54-1.570.30811500.28682632X-RAY DIFFRACTION98
1.57-1.610.28811280.24592715X-RAY DIFFRACTION99
1.61-1.650.25211390.24882704X-RAY DIFFRACTION99
1.65-1.70.27471540.2372681X-RAY DIFFRACTION99
1.7-1.750.25561260.23042713X-RAY DIFFRACTION99
1.75-1.80.24651580.22062664X-RAY DIFFRACTION99
1.8-1.870.24281420.2042699X-RAY DIFFRACTION99
1.87-1.940.20091420.22721X-RAY DIFFRACTION99
1.94-2.030.21231420.19552695X-RAY DIFFRACTION98
2.03-2.140.21741370.19982614X-RAY DIFFRACTION97
2.14-2.270.21831520.19212729X-RAY DIFFRACTION99
2.27-2.440.22921390.20062723X-RAY DIFFRACTION99
2.44-2.690.24271480.20482707X-RAY DIFFRACTION99
2.69-3.080.25671510.20962717X-RAY DIFFRACTION99
3.08-3.880.17781300.17872702X-RAY DIFFRACTION97
3.88-37.70.1831510.16082774X-RAY DIFFRACTION99

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