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- PDB-1sjn: Mycobacterium tuberculosis dUTPase complexed with magnesium and a... -

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Basic information

Entry
Database: PDB / ID: 1sjn
TitleMycobacterium tuberculosis dUTPase complexed with magnesium and alpha,beta-imido-dUTP
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
2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE / NITRATE ION / Deoxyuridine 5'-triphosphate nucleotidohydrolase / Deoxyuridine 5'-triphosphate nucleotidohydrolase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _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
B: Deoxyuridine 5'-triphosphate nucleotidohydrolase
C: Deoxyuridine 5'-triphosphate nucleotidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,43912
Polymers52,7193
Non-polymers1,7219
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13960 Å2
ΔGint-73 kcal/mol
Surface area15580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.521, 78.506, 94.509
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a homotrimer. It is contained within the asymmetric unit.

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 17572.871 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: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3)
References: UniProt: P0A552, UniProt: P9WNS5*PLUS, dUTP diphosphatase

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Non-polymers , 5 types, 215 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 467.157 Da / Num. of mol.: 3 / 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: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.41 Å3/Da / Density % sol: 48.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 3350, magnesium nitrate, TRIS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.1271 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 13, 2003
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 1.8→90 Å / Num. all: 39997 / Num. obs: 39997 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 32.6 Å2 / Rsym value: 0.069 / Net I/σ(I): 20
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 5.7 / Num. unique all: 3975 / Rsym value: 0.325 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SIX

1six


Resolution: 1.8→60.86 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.168 / SU ML: 0.068 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19765 2016 5 %RANDOM
Rwork0.16823 ---
all0.17 37906 --
obs0.16973 37906 98.83 %-
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: 24.076 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å20 Å20 Å2
2--0.91 Å20 Å2
3---0.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.109 Å0.115 Å
Refinement stepCycle: LAST / Resolution: 1.8→60.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3037 0 103 206 3346
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0213212
X-RAY DIFFRACTIONr_bond_other_d0.0020.023073
X-RAY DIFFRACTIONr_angle_refined_deg1.9492.0344400
X-RAY DIFFRACTIONr_angle_other_deg0.91537073
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5325411
X-RAY DIFFRACTIONr_chiral_restr0.1240.2527
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023539
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02604
X-RAY DIFFRACTIONr_nbd_refined0.1970.2467
X-RAY DIFFRACTIONr_nbd_other0.2620.23518
X-RAY DIFFRACTIONr_nbtor_other0.0830.22107
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2172
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2620.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3130.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2580.29
X-RAY DIFFRACTIONr_mcbond_it1.1361.52062
X-RAY DIFFRACTIONr_mcangle_it1.99623310
X-RAY DIFFRACTIONr_scbond_it2.97431150
X-RAY DIFFRACTIONr_scangle_it4.8634.51090
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.252 166
Rwork0.208 2757
Refinement TLS params.Method: refined / Origin x: 13.275 Å / Origin y: -8.773 Å / Origin z: -8.998 Å
111213212223313233
T0.0918 Å2-0.0035 Å20.0346 Å2-0.0228 Å2-0.0287 Å2--0.0468 Å2
L0.52 °2-0.0127 °2-0.2226 °2-1.149 °20.1289 °2--1.1231 °2
S-0.0794 Å °0.1007 Å °-0.1605 Å °-0.2304 Å °-0.0531 Å °-0.007 Å °0.2387 Å °-0.0816 Å °0.1325 Å °

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