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- PDB-8uvz: Bacillus subtilis DHFR bound to NADP+ and folate -

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Basic information

Entry
Database: PDB / ID: 8uvz
TitleBacillus subtilis DHFR bound to NADP+ and folate
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / pterin / hydride transfer
Function / homology
Function and homology information


glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding
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 speciesBacillus subtilis (bacteria)
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: Bacillus subtilis DHFR bound to NADP+ and folate
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)20,6234
Polymers19,2001
Non-polymers1,4233
Water5,423301
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.450, 88.450, 37.265
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

#1: Protein Dihydrofolate reductase


Mass: 19199.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: dfrA / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A164XFT9
#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-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.19 Å3/Da / Density % sol: 43.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 10% PEG4000, 100 mM sodium acetate pH=5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 4, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 0.93→44.22 Å / Num. obs: 110282 / % possible obs: 100 % / Redundancy: 11.3 % / Biso Wilson estimate: 9.12 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.065 / Net I/σ(I): 20.9
Reflection shellResolution: 0.93→0.95 Å / Redundancy: 9.3 % / Mean I/σ(I) obs: 2.8 / Num. unique obs: 5386 / CC1/2: 0.873 / Rrim(I) all: 0.657 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MOSFLMdata reduction
Aimlessdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.93→44.22 Å / SU ML: 0.072 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 9.6008
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1233 5504 4.99 %
Rwork0.1103 104744 -
obs0.1109 110248 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.93 Å2
Refinement stepCycle: LAST / Resolution: 0.93→44.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1298 0 96 301 1695
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01332006
X-RAY DIFFRACTIONf_angle_d1.67122758
X-RAY DIFFRACTIONf_chiral_restr0.0961261
X-RAY DIFFRACTIONf_plane_restr0.0142367
X-RAY DIFFRACTIONf_dihedral_angle_d15.8625779
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.93-0.940.22831770.20153415X-RAY DIFFRACTION98.71
0.94-0.960.18721810.17753489X-RAY DIFFRACTION100
0.96-0.970.1691990.16493449X-RAY DIFFRACTION100
0.97-0.980.14831610.14613521X-RAY DIFFRACTION100
0.98-0.990.13991790.13233419X-RAY DIFFRACTION100
0.99-1.010.13612090.11973504X-RAY DIFFRACTION100
1.01-1.020.12181910.10683440X-RAY DIFFRACTION100
1.02-1.040.11491810.09983498X-RAY DIFFRACTION100
1.04-1.050.11911610.09693474X-RAY DIFFRACTION100
1.05-1.070.12451850.09263472X-RAY DIFFRACTION100
1.07-1.090.09771690.09183485X-RAY DIFFRACTION100
1.09-1.110.12422090.093475X-RAY DIFFRACTION99.97
1.11-1.130.09991960.08613487X-RAY DIFFRACTION100
1.13-1.150.11682020.08633436X-RAY DIFFRACTION100
1.15-1.180.11361830.08233477X-RAY DIFFRACTION100
1.18-1.20.08161490.08343531X-RAY DIFFRACTION100
1.2-1.230.10292160.08213444X-RAY DIFFRACTION99.97
1.23-1.270.1081710.0833484X-RAY DIFFRACTION100
1.27-1.30.09711650.08623505X-RAY DIFFRACTION100
1.3-1.350.09631410.08773552X-RAY DIFFRACTION100
1.35-1.390.11281660.09323519X-RAY DIFFRACTION100
1.39-1.450.11192070.09693459X-RAY DIFFRACTION100
1.45-1.520.10341990.09223492X-RAY DIFFRACTION100
1.52-1.60.10311980.09373470X-RAY DIFFRACTION100
1.6-1.70.10911570.10373535X-RAY DIFFRACTION100
1.7-1.830.12312140.1093470X-RAY DIFFRACTION100
1.83-2.010.10682000.10853512X-RAY DIFFRACTION100
2.01-2.30.12591980.11553513X-RAY DIFFRACTION100
2.3-2.90.1591680.13483573X-RAY DIFFRACTION100
2.9-44.220.13921720.12523644X-RAY DIFFRACTION99.95

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