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- PDB-8jsy: Dihydrofolate reductase-like enzyme from Leptospira interrogans -

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Basic information

Entry
Database: PDB / ID: 8jsy
TitleDihydrofolate reductase-like enzyme from Leptospira interrogans
ComponentsDihydrofolate reductase family protein
KeywordsOXIDOREDUCTASE / Dihydrofolate reductase-like enzyme / spirochete
Function / homologyACETATE ION / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / :
Function and homology information
Biological speciesLeptospira interrogans serovar Pomona (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.55 Å
AuthorsWangkanont, K.
Funding support Thailand, 1items
OrganizationGrant numberCountry
Other government Thailand
CitationJournal: To Be Published
Title: Dihydrofolate reductase-like enzyme from Leptospira interrogans
Authors: Wangkanont, K.
History
DepositionJun 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2024Provider: 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 family protein
B: Dihydrofolate reductase family protein
C: Dihydrofolate reductase family protein
D: Dihydrofolate reductase family protein
E: Dihydrofolate reductase family protein
F: Dihydrofolate reductase family protein
G: Dihydrofolate reductase family protein
H: Dihydrofolate reductase family protein
I: Dihydrofolate reductase family protein
J: Dihydrofolate reductase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,88772
Polymers226,07710
Non-polymers14,81062
Water7,440413
1
A: Dihydrofolate reductase family protein
B: Dihydrofolate reductase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,70510
Polymers45,2152
Non-polymers2,4908
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8330 Å2
ΔGint-95 kcal/mol
Surface area16900 Å2
MethodPISA
2
C: Dihydrofolate reductase family protein
D: Dihydrofolate reductase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,91014
Polymers45,2152
Non-polymers2,69512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8860 Å2
ΔGint-99 kcal/mol
Surface area17500 Å2
MethodPISA
3
F: Dihydrofolate reductase family protein
hetero molecules

E: Dihydrofolate reductase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,09014
Polymers45,2152
Non-polymers2,87412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area8720 Å2
ΔGint-118 kcal/mol
Surface area17030 Å2
MethodPISA
4
G: Dihydrofolate reductase family protein
H: Dihydrofolate reductase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,32815
Polymers45,2152
Non-polymers3,11213
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9820 Å2
ΔGint-131 kcal/mol
Surface area16870 Å2
MethodPISA
5
I: Dihydrofolate reductase family protein
J: Dihydrofolate reductase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,85419
Polymers45,2152
Non-polymers3,63917
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10510 Å2
ΔGint-162 kcal/mol
Surface area18350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.242, 137.357, 236.873
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

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Protein , 1 types, 10 molecules ABCDEFGHIJ

#1: Protein
Dihydrofolate reductase family protein


Mass: 22607.734 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira interrogans serovar Pomona (bacteria)
Gene: IQB77_11460 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner (DE3) / References: UniProt: A0A8I0PU34

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Non-polymers , 5 types, 475 molecules

#2: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 34 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.16 Å3/Da / Density % sol: 61.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 100 mM sodium acetate, 200 mM ammonium sulfate, 25-27% PEG 550 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.99999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 20, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2.55→29.9 Å / Num. obs: 91312 / % possible obs: 99.8 % / Redundancy: 5.7 % / Biso Wilson estimate: 60.52 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.025 / Rrim(I) all: 0.061 / Χ2: 0.95 / Net I/σ(I): 17.5
Reflection shellResolution: 2.55→2.59 Å / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4479 / CC1/2: 0.688 / Rpim(I) all: 0.411 / Rrim(I) all: 0.807 / Χ2: 1.05 / % possible all: 99.9

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Processing

Software
NameVersionClassification
XDSMar 15, 2019 BUILT=20191211data reduction
Aimless0.7.3data scaling
PHENIX1.14_3260phasing
PHENIX1.14_3260model building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.55→29.9 Å / SU ML: 0.3667 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.5496
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2474 4372 4.8 %
Rwork0.1966 86688 -
obs0.1991 91060 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.65 Å2
Refinement stepCycle: LAST / Resolution: 2.55→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15448 0 887 413 16748
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009216735
X-RAY DIFFRACTIONf_angle_d1.231422662
X-RAY DIFFRACTIONf_chiral_restr0.06482411
X-RAY DIFFRACTIONf_plane_restr0.00912726
X-RAY DIFFRACTIONf_dihedral_angle_d25.96615950
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.640.38414240.28838528X-RAY DIFFRACTION99.24
2.64-2.750.35824100.27718612X-RAY DIFFRACTION99.7
2.75-2.870.32974420.26528547X-RAY DIFFRACTION99.89
2.87-3.020.32264500.26818596X-RAY DIFFRACTION99.82
3.02-3.210.31024260.25258619X-RAY DIFFRACTION99.83
3.21-3.460.29324470.23428624X-RAY DIFFRACTION99.81
3.46-3.810.26954200.20548670X-RAY DIFFRACTION99.67
3.81-4.360.21574460.17338695X-RAY DIFFRACTION99.6
4.36-5.480.19754710.14578741X-RAY DIFFRACTION99.71
5.48-29.90.20054360.17089056X-RAY DIFFRACTION99.33

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