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- PDB-8jsv: Dihydrofolate reductase-like enzyme from Leptospira interrogans (... -

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Basic information

Entry
Database: PDB / ID: 8jsv
TitleDihydrofolate reductase-like enzyme from Leptospira interrogans (selenomethionine derivative)
ComponentsDihydrofolate reductase family protein
KeywordsOXIDOREDUCTASE / dihydrofolate reductase-like enzyme / spirochete
Function / homologyNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / :
Function and homology information
Biological speciesLeptospira interrogans serovar Pomona (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.55 Å
AuthorsChandit, C. / Wangkanont, K.
Funding support Thailand, 1items
OrganizationGrant numberCountry
Other government Thailand
CitationJournal: To Be Published
Title: Dihydrofolate reductase-like enzyme from Leptospira interrogans (selenomethionine derivative)
Authors: Chandit, C. / 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

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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)243,83872
Polymers228,42210
Non-polymers15,41662
Water5,819323
1
A: Dihydrofolate reductase family protein
B: Dihydrofolate reductase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,36612
Polymers45,6842
Non-polymers2,68210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8310 Å2
ΔGint-111 kcal/mol
Surface area17010 Å2
MethodPISA
2
C: Dihydrofolate reductase family protein
D: Dihydrofolate reductase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,03516
Polymers45,6842
Non-polymers3,35114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9870 Å2
ΔGint-112 kcal/mol
Surface area17550 Å2
MethodPISA
3
F: Dihydrofolate reductase family protein
hetero molecules

E: Dihydrofolate reductase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,93915
Polymers45,6842
Non-polymers3,25513
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area8920 Å2
ΔGint-108 kcal/mol
Surface area16930 Å2
MethodPISA
4
G: Dihydrofolate reductase family protein
H: Dihydrofolate reductase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,70114
Polymers45,6842
Non-polymers3,01612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9660 Å2
ΔGint-139 kcal/mol
Surface area17050 Å2
MethodPISA
5
I: Dihydrofolate reductase family protein
J: Dihydrofolate reductase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,79715
Polymers45,6842
Non-polymers3,11213
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9170 Å2
ΔGint-95 kcal/mol
Surface area18320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.900, 138.329, 236.699
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

#1: Protein
Dihydrofolate reductase family protein


Mass: 22842.211 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira interrogans serovar Pomona (bacteria)
Gene: IQB77_11460 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express Crystal / References: UniProt: A0A8I0PU34
#2: Chemical...
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 21 / 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.: 31 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 3.14 Å3/Da / Density % sol: 60.81 %
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: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 2, 2020
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.55→29.98 Å / Num. obs: 175482 / % possible obs: 99.9 % / Redundancy: 14.8 % / Biso Wilson estimate: 55.94 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.16 / Rpim(I) all: 0.043 / Rrim(I) all: 0.166 / Χ2: 0.95 / Net I/σ(I): 11.7
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 15.2 % / Rmerge(I) obs: 2.081 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 68438 / CC1/2: 0.724 / Rpim(I) all: 0.549 / Rrim(I) all: 2.177 / Χ2: 0.78 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSMar 15, 2019 BUILT=20191211data reduction
Aimless0.7.3data scaling
PHENIX1.14_3260phasing
PHENIX1.20.1_4487model building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: SAD / Resolution: 2.55→29.98 Å / SU ML: 0.3463 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.1447
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2345 8407 4.79 %
Rwork0.1909 167075 -
obs0.193 175482 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.93 Å2
Refinement stepCycle: LAST / Resolution: 2.55→29.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15448 0 897 323 16668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010216787
X-RAY DIFFRACTIONf_angle_d1.224522724
X-RAY DIFFRACTIONf_chiral_restr0.06812415
X-RAY DIFFRACTIONf_plane_restr0.01012736
X-RAY DIFFRACTIONf_dihedral_angle_d20.9715977
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.580.35482830.29895664X-RAY DIFFRACTION100
2.58-2.610.32782670.28635522X-RAY DIFFRACTION100
2.61-2.640.33662770.27345589X-RAY DIFFRACTION100
2.64-2.670.34042740.27555580X-RAY DIFFRACTION100
2.67-2.710.30252830.28095605X-RAY DIFFRACTION100
2.71-2.750.31852540.26935552X-RAY DIFFRACTION100
2.75-2.790.2992990.26485520X-RAY DIFFRACTION100
2.79-2.830.30132790.27255619X-RAY DIFFRACTION100
2.83-2.870.33382770.26955503X-RAY DIFFRACTION100
2.87-2.920.3482770.27525623X-RAY DIFFRACTION100
2.92-2.970.3193060.26255502X-RAY DIFFRACTION100
2.97-3.020.29952880.24695586X-RAY DIFFRACTION100
3.02-3.080.25412730.24055557X-RAY DIFFRACTION100
3.08-3.140.29342860.23315620X-RAY DIFFRACTION100
3.14-3.210.30422510.2385525X-RAY DIFFRACTION100
3.21-3.290.29553190.23375565X-RAY DIFFRACTION100
3.29-3.370.2972730.21625601X-RAY DIFFRACTION100
3.37-3.460.25782870.21585531X-RAY DIFFRACTION100
3.46-3.560.29272540.2055590X-RAY DIFFRACTION100
3.56-3.680.21632990.1915555X-RAY DIFFRACTION99.98
3.68-3.810.25612480.1865579X-RAY DIFFRACTION100
3.81-3.960.21733240.18085547X-RAY DIFFRACTION100
3.96-4.140.22172610.1665580X-RAY DIFFRACTION100
4.14-4.360.18882760.14885569X-RAY DIFFRACTION100
4.36-4.630.17893270.13475549X-RAY DIFFRACTION100
4.63-4.980.17652650.13585588X-RAY DIFFRACTION100
4.98-5.480.18942940.15475535X-RAY DIFFRACTION100
5.48-6.270.19972860.16895564X-RAY DIFFRACTION100
6.27-7.870.20812730.16675568X-RAY DIFFRACTION100
7.88-29.980.15352470.15295587X-RAY DIFFRACTION99.49

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