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- PDB-1smc: Mycobacterium tuberculosis dUTPase complexed with dUTP in the abs... -

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Basic information

Entry
Database: PDB / ID: 1smc
TitleMycobacterium tuberculosis dUTPase complexed with dUTP in the absence of metal ion.
ComponentsDeoxyuridine 5'-triphosphate nucleotidohydrolase
KeywordsHYDROLASE / jelly-roll / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
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
DEOXYURIDINE-5'-TRIPHOSPHATE / NITRATE ION / Deoxyuridine 5'-triphosphate nucleotidohydrolase / Deoxyuridine 5'-triphosphate nucleotidohydrolase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsSawaya, M.R. / Chan, S. / Segelke, B. / Lekin, T. / Krupka, H. / Cho, U.S. / Kim, M.-Y. / So, M. / Kim, C.-Y. / Naranjo, C.M. ...Sawaya, M.R. / Chan, S. / Segelke, B. / Lekin, T. / Krupka, H. / Cho, U.S. / Kim, M.-Y. / So, M. / Kim, C.-Y. / Naranjo, C.M. / Rogers, Y.C. / Park, M.S. / Waldo, G.S. / Pashkov, I. / Cascio, D. / Yeates, T.O. / Perry, J.L. / Terwilliger, T.C. / Eisenberg, D. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal structure of the Mycobacterium tuberculosis dUTPase: insights into the catalytic mechanism.
Authors: Chan, S. / Segelke, B. / Lekin, T. / Krupka, H. / Cho, U.S. / Kim, M.-Y. / So, M. / Kim, C.-Y. / Naranjo, C.M. / Rogers, Y.C. / Park, M.S. / Waldo, G.S. / Pashkov, I. / Cascio, D. / Perry, J.L. / Sawaya, M.R.
History
DepositionMar 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,81010
Polymers53,9773
Non-polymers1,8337
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13030 Å2
ΔGint-36 kcal/mol
Surface area15320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.595, 77.697, 94.781
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a homo-trimer. It is contained within the asymmetric unit.

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Components

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


Mass: 17992.314 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: DUT, RV2697C, MT2771, MTCY05A6.18C, MB2716C / Plasmid: modified pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21PRO
References: UniProt: P0A552, UniProt: P9WNS5*PLUS, dUTP diphosphatase
#2: Chemical ChemComp-DUT / DEOXYURIDINE-5'-TRIPHOSPHATE


Mass: 468.142 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H15N2O14P3
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.51 Å3/Da / Density % sol: 50.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 3350, ammonium nitrate, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 2, 2002 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→80 Å / Num. all: 27903 / Num. obs: 27903 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.1 % / Biso Wilson estimate: 34.9 Å2 / Rsym value: 0.109 / Net I/σ(I): 22.7
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 11.1 % / Mean I/σ(I) obs: 5.8 / Num. unique all: 2746 / Rsym value: 0.453 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: M. tuberculosis dUTPase complexed with dUMP and magnesium.

Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.845 / SU ML: 0.105 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.208 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20675 2525 9.9 %RANDOM
Rwork0.16549 ---
all0.16959 23083 --
obs0.16959 23083 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.246 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å20 Å2
2---1.33 Å20 Å2
3---1.92 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2928 0 112 220 3260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0213112
X-RAY DIFFRACTIONr_bond_other_d0.0030.022996
X-RAY DIFFRACTIONr_angle_refined_deg2.2462.0394263
X-RAY DIFFRACTIONr_angle_other_deg1.09136893
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3755393
X-RAY DIFFRACTIONr_chiral_restr0.1140.2510
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023387
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02583
X-RAY DIFFRACTIONr_nbd_refined0.1880.2841
X-RAY DIFFRACTIONr_nbd_other0.2650.23552
X-RAY DIFFRACTIONr_nbtor_other0.1610.23017
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2187
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3530.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.29
X-RAY DIFFRACTIONr_mcbond_it1.0331.51984
X-RAY DIFFRACTIONr_mcangle_it1.79123191
X-RAY DIFFRACTIONr_scbond_it2.92131128
X-RAY DIFFRACTIONr_scangle_it4.9324.51072
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.224 167
Rwork0.171 1682
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)
10.37180.09050.23620.78820.30340.67010.00270.031-0.0721-0.1241-0.02570.00910.0432-0.01410.0230.08290.00630.00260.0873-0.01650.020313.257-9.033-8.816
20.9605-0.2046-0.27570.70970.15720.49860.0264-0.07670.02020.0259-0.00770.0756-0.0243-0.0776-0.01870.0681-0.00180.01120.0974-0.01640.0052.7242.4712.437
30.7566-0.14680.4550.5278-0.04490.45560.0382-0.0024-0.0450.0657-0.0103-0.0562-0.00390.034-0.02790.0731-0.00220.00450.10250.00120.022621.640.3825.634
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 13024 - 150
2X-RAY DIFFRACTION2BB4 - 13024 - 150
3X-RAY DIFFRACTION3CC4 - 13024 - 150

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