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- PDB-2py4: Full length structure of the Mycobacterium tuberculosis dUTPase c... -

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Basic information

Entry
Database: PDB / ID: 2py4
TitleFull length structure of the Mycobacterium tuberculosis dUTPase complexed with magnesium and alpha,beta-imido-dUTP.
ComponentsDeoxyuridine 5'-triphosphate nucleotidohydrolase
KeywordsHYDROLASE / JELLY-ROLL / enzyme-ligand complex
Function / homology
Function and homology information


dUTP metabolic process / dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / magnesium ion binding
Similarity search - Function
Deoxyuridine triphosphate nucleotidohydrolase / Deoxyuridine triphosphatase (dUTPase) / Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE / Deoxyuridine 5'-triphosphate nucleotidohydrolase / Deoxyuridine 5'-triphosphate nucleotidohydrolase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsBarabas, O. / Nagy, N. / Takacs, E. / Vertessy, B.G.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2008
Title: Active site of mycobacterial dUTPase: structural characteristics and a built-in sensor.
Authors: Varga, B. / Barabas, O. / Takacs, E. / Nagy, N. / Nagy, P. / Vertessy, B.G.
History
DepositionMay 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deoxyuridine 5'-triphosphate nucleotidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6064
Polymers17,9921
Non-polymers6143
Water2,378132
1
A: Deoxyuridine 5'-triphosphate nucleotidohydrolase
hetero molecules

A: Deoxyuridine 5'-triphosphate nucleotidohydrolase
hetero molecules

A: Deoxyuridine 5'-triphosphate nucleotidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,81812
Polymers53,9773
Non-polymers1,8419
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area18150 Å2
ΔGint-69 kcal/mol
Surface area14200 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)54.591, 54.591, 83.051
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-201-

TRS

21A-201-

TRS

31A-796-

HOH

41A-866-

HOH

51A-893-

HOH

61A-908-

HOH

DetailsThe biological assembly is a trimer generated from the monomer in the asymmetric unit by applying the transformation matrices: rotation-1: | 1 0 0| | 0 1 0| | 0 0 1| translation-1: (0 0 0 ) rotation-2: |-0.5 -0.866 0| |0.866 -0.5 0| | 0 0 1| translation-2: (54.29 0 0 ) and rotation-3: |-0.5 0.866 0| |-0.866 -0.5 0| | 0 0 1| translation-3: (27.3 47.28 0 )

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Components

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


Mass: 17992.314 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: dut / Plasmid: pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: P0A552, UniProt: P9WNS5*PLUS, dUTP diphosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-DUP / 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O

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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: 1.98 Å3/Da / Density % sol: 38.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.5M ammonium sulfate, 0.1M Tris/HCl, 12% glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.49→20 Å / Num. all: 21589 / Num. obs: 21589 / % possible obs: 94.1 % / Observed criterion σ(I): -3 / Redundancy: 3.95 % / Biso Wilson estimate: 19.3 Å2 / Rsym value: 4.1 / Net I/σ(I): 24.57
Reflection shellResolution: 1.49→1.58 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 2595 / Rsym value: 34.8 / % possible all: 70.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
START(RIGAKU)data collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1MQ7

1mq7


Resolution: 1.49→19.44 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.184 / SU ML: 0.045 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16997 1109 5.1 %RANDOM
Rwork0.1442 ---
obs0.14553 20480 94.09 %-
all-20480 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.838 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20.03 Å20 Å2
2--0.06 Å20 Å2
3----0.08 Å2
Refine analyzeLuzzati coordinate error obs: 0.141 Å
Refinement stepCycle: LAST / Resolution: 1.49→19.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1081 0 37 132 1250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0211134
X-RAY DIFFRACTIONr_angle_refined_deg1.9922.0251552
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2745152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.28422.536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.07315162
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.368159
X-RAY DIFFRACTIONr_chiral_restr0.1480.2186
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02834
X-RAY DIFFRACTIONr_nbd_refined0.2130.2475
X-RAY DIFFRACTIONr_nbtor_refined0.3210.2806
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.296
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.2121
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.245
X-RAY DIFFRACTIONr_mcbond_it2.1643768
X-RAY DIFFRACTIONr_mcangle_it3.137201207
X-RAY DIFFRACTIONr_scbond_it4.97620392
X-RAY DIFFRACTIONr_scangle_it6.05450345
LS refinement shellResolution: 1.49→1.529 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 52 -
Rwork0.255 927 -
obs-979 57.32 %
Refinement TLS params.Method: refined / Origin x: 20.85 Å / Origin y: 17.7538 Å / Origin z: 39.5449 Å
111213212223313233
T-0.009 Å20.0016 Å2-0.0007 Å2--0.0067 Å2-0.0045 Å2---0.0143 Å2
L0.227 °2-0.0186 °20.0253 °2-0.2704 °2-0.0256 °2--0.0377 °2
S0.0107 Å °0.0146 Å °0.0207 Å °-0.0223 Å °-0.0045 Å °0.009 Å °0.0024 Å °-0.0116 Å °-0.0062 Å °

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