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- PDB-8p8o: M. tuberculosis dUTPase - Stl1-159 (StlNT) complex structure -

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Basic information

Entry
Database: PDB / ID: 8p8o
TitleM. tuberculosis dUTPase - Stl1-159 (StlNT) complex structure
Components
  • Deoxyuridine 5'-triphosphate nucleotidohydrolase
  • Orf20
KeywordsHYDROLASE / complex / inhibition
Function / homology
Function and homology information


dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / magnesium ion binding / DNA binding
Similarity search - Function
Deoxyuridine triphosphate nucleotidohydrolase / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily
Similarity search - Domain/homology
Deoxyuridine 5'-triphosphate nucleotidohydrolase / Orf20
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsBenedek, A. / Leveles, I. / Toth, Z.S. / Harmat, V. / Vertessy, B.G.
Funding support Hungary, 1items
OrganizationGrant numberCountry
National Research Development and Innovation Office (NKFIH)K119493 Hungary
CitationJournal: Sci Rep / Year: 2024
Title: The homodimerization domain of the Stl repressor is crucial for efficient inhibition of mycobacterial dUTPase.
Authors: Toth, Z.S. / Leveles, I. / Nyiri, K. / Nagy, G.N. / Harmat, V. / Jaroentomeechai, T. / Ozohanics, O. / Miller, R.L. / Alvarez, M.B. / Vertessy, B.G. / Benedek, A.
History
DepositionJun 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 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: Deoxyuridine 5'-triphosphate nucleotidohydrolase
B: Deoxyuridine 5'-triphosphate nucleotidohydrolase
C: Deoxyuridine 5'-triphosphate nucleotidohydrolase
D: Deoxyuridine 5'-triphosphate nucleotidohydrolase
E: Deoxyuridine 5'-triphosphate nucleotidohydrolase
G: Deoxyuridine 5'-triphosphate nucleotidohydrolase
H: Orf20
I: Orf20
J: Orf20
F: Orf20
K: Orf20
L: Orf20


Theoretical massNumber of molelcules
Total (without water)222,25612
Polymers222,25612
Non-polymers00
Water00
1
A: Deoxyuridine 5'-triphosphate nucleotidohydrolase
B: Deoxyuridine 5'-triphosphate nucleotidohydrolase
C: Deoxyuridine 5'-triphosphate nucleotidohydrolase
J: Orf20
F: Orf20
K: Orf20


Theoretical massNumber of molelcules
Total (without water)111,1286
Polymers111,1286
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Deoxyuridine 5'-triphosphate nucleotidohydrolase
E: Deoxyuridine 5'-triphosphate nucleotidohydrolase
G: Deoxyuridine 5'-triphosphate nucleotidohydrolase
H: Orf20
I: Orf20
L: Orf20


Theoretical massNumber of molelcules
Total (without water)111,1286
Polymers111,1286
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.669, 123.820, 170.229
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Deoxyuridine 5'-triphosphate nucleotidohydrolase / dUTPase / dUTP pyrophosphatase


Mass: 17992.314 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Our dUTPase construct contained an N-terminal His-tag which is not visible on the electron density map. We would like to ask you to start the numbering of dUTPase residues from the second ...Details: Our dUTPase construct contained an N-terminal His-tag which is not visible on the electron density map. We would like to ask you to start the numbering of dUTPase residues from the second methionine in the sequence.
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: dut, ERS007657_03143, ERS007661_03256, ERS007663_01934, ERS007665_02282, ERS007670_03268, ERS007679_02947, ERS007681_03276, ERS007720_02832, ERS007722_03847, ERS007739_03502, ERS007741_03306, ...Gene: dut, ERS007657_03143, ERS007661_03256, ERS007663_01934, ERS007665_02282, ERS007670_03268, ERS007679_02947, ERS007681_03276, ERS007720_02832, ERS007722_03847, ERS007739_03502, ERS007741_03306, ERS024276_02245, ERS027646_03433, ERS027659_03029, ERS027661_04079
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A045IIQ9, dUTP diphosphatase
#2: Protein
Orf20


Mass: 19050.324 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: We would like to kindly ask you to start the numbering of Stl residues from the first methionine in the sequence. An N-terminal GST tag was cleaved from our construct before crystallization ...Details: We would like to kindly ask you to start the numbering of Stl residues from the first methionine in the sequence. An N-terminal GST tag was cleaved from our construct before crystallization and its remaining N-terminal residues are not visible on the electron density map.
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9F0J8
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: 2.52 Å3/Da / Density % sol: 51.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M TRIS, 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 16, 2021
RadiationMonochromator: Double Crystal Si111 with LN2 closed loop cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→46.38 Å / Num. obs: 30380 / % possible obs: 97.5 % / Redundancy: 5.24 % / Biso Wilson estimate: 126.15 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.156 / Net I/σ(I): 13.92
Reflection shellResolution: 3.41→3.5 Å / Redundancy: 5.21 % / Mean I/σ(I) obs: 0.48 / Num. unique obs: 2113 / CC1/2: 0.314 / Rrim(I) all: 6.237 / % possible all: 93.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→46.38 Å / SU ML: 0.9401 / Cross valid method: FREE R-VALUE / Phase error: 40.6991
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2856 1991 6.61 %
Rwork0.2439 28141 -
obs0.2467 30132 96.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 138.31 Å2
Refinement stepCycle: LAST / Resolution: 3.4→46.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11820 0 0 0 11820
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001912045
X-RAY DIFFRACTIONf_angle_d0.449316433
X-RAY DIFFRACTIONf_chiral_restr0.04091923
X-RAY DIFFRACTIONf_plane_restr0.00412137
X-RAY DIFFRACTIONf_dihedral_angle_d8.81674197
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.490.57331190.54971739X-RAY DIFFRACTION85.35
3.49-3.580.51021410.4771957X-RAY DIFFRACTION95.84
3.58-3.690.45981250.47781943X-RAY DIFFRACTION94.39
3.69-3.80.49171350.39011988X-RAY DIFFRACTION96.9
3.8-3.940.43151350.37871923X-RAY DIFFRACTION94.62
3.94-4.10.38551430.33092010X-RAY DIFFRACTION98.09
4.1-4.280.30971510.28342018X-RAY DIFFRACTION98.55
4.28-4.510.31441310.23742053X-RAY DIFFRACTION98.78
4.51-4.790.26621570.21622045X-RAY DIFFRACTION99.41
4.79-5.160.29691400.20472058X-RAY DIFFRACTION99.23
5.16-5.680.27251510.21072062X-RAY DIFFRACTION99.59
5.68-6.50.25271420.22252102X-RAY DIFFRACTION99.51
6.5-8.180.22891550.21662095X-RAY DIFFRACTION99.21
8.18-46.380.22251660.18192148X-RAY DIFFRACTION97.35
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.04604262623-1.039512807051.229948309875.95230860174.540243774463.952385625540.3991572357240.319908986788-0.350298403973-0.597000593905-0.7435494270141.43418006876-0.04884919334890.5665201455140.2804112545171.06299445719-0.0523244129678-0.03169822913781.000665651120.4538293546121.3687164389644.0839838324-14.1376335108-33.8355257911
29.068629416195.70994486484-3.142230865716.27778643375-2.094013350674.17937052482-0.2613452605410.313213043204-0.09471709668130.4112917081840.127333546195-0.4632332417310.2313838862930.05954127366790.1208879843841.265647290950.1151106777680.0294431748120.8003468811310.009980429969721.0016880369756.8193864707-4.30237048679-20.5660852346
32.644604988930.460877582339-4.091518655327.26429845127-3.595568161989.86571673134-0.385015606437-0.576221988412-0.231048232235-0.6669222385461.017810335730.2336033504020.6779966148310.860680511198-0.6502082334330.818398312149-0.1877298896470.1006654453180.970140569209-0.3505864880681.4345832131943.2129787795-18.1817123712-17.2552804856
43.02462303475-1.432121051611.804761514886.924032318624.931418410416.23930614062-0.898612043729-0.528145701809-0.0799648083982-0.2201085944820.3373491722221.23118498967-0.598329806038-0.8413301624220.8152062503591.05105501492-0.0525646679695-0.2487872247221.429398235630.1356991653671.393353360746.390040234619.83098059747-8.24514520854
56.262250828621.16970037669-5.527441801663.36967427853-2.539445086456.595243363130.327213332220.8438823403611.204097343620.4298022146740.736135086729-0.321467477799-0.638447576913-1.23235249875-1.095627929510.7101939607440.187169258252-0.04996884389631.380302821810.007425220730911.226062188097.5778763451510.1565845912-27.3797971656
64.076877584754.139115481370.03137918326312.717722354730.8520633349434.441676505650.179211142196-0.8900363103181.140777453570.26453706256-0.593605009677-0.477784180891-0.500197290142-0.693592127355-0.05110583672470.9275933736520.1685669945040.09986218248181.294821480720.125027328931.42163492336-4.33513601423-0.884450185302-20.9987450946
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 25 through 29) or (chain 'A' and resid 83 through 86) or (chain 'A' and resid 80 through 88) or (chain 'A' and resid 106 through 113) or (chain 'A' and resid 130 through 134)AA25 - 13123 - 129
22(chain 'B' and resid 25 through 29) or (chain 'B' and resid 83 through 86) or (chain 'B' and resid 80 through 88) or (chain 'B' and resid 106 through 113) or (chain 'B' and resid 130 through 134)BB25 - 13023 - 128
33(chain 'C' and resid 25 through 29) or (chain 'C' and resid 83 through 86) or (chain 'C' and resid 80 through 88) or (chain 'C' and resid 106 through 113) or (chain 'C' and resid 130 through 134)CC25 - 13424 - 133
44(chain 'D' and resid 25 through 29) or (chain 'D' and resid 83 through 86) or (chain 'D' and resid 80 through 88) or (chain 'D' and resid 106 through 113) or (chain 'D' and resid 130 through 134)DD25 - 13024 - 129
55(chain 'E' and resid 25 through 29) or (chain 'E' and resid 83 through 86) or (chain 'E' and resid 80 through 88) or (chain 'E' and resid 106 through 113) or (chain 'E' and resid 130 through 134)EE25 - 13424 - 132
66(chain 'G' and resid 25 through 29) or (chain 'G' and resid 83 through 86) or (chain 'G' and resid 80 through 88) or (chain 'G' and resid 106 through 113) or (chain 'G' and resid 130 through 134)GF25 - 13224 - 131

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