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- PDB-1mq7: CRYSTAL STRUCTURE OF DUTPASE FROM MYCOBACTERIUM TUBERCULOSIS (RV2697C) -

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Basic information

Entry
Database: PDB / ID: 1mq7
TitleCRYSTAL STRUCTURE OF DUTPASE FROM MYCOBACTERIUM TUBERCULOSIS (RV2697C)
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 nucleotidohydrolase / Deoxyuridine 5'-triphosphate nucleotidohydrolase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSawaya, M.R. / Chan, S. / Segelke, B.W. / Lekin, T. / Heike, K. / Cho, U.S. / Naranjo, C. / Perry, L.J. / Yeates, T.O. / Eisenberg, D. / TB Structural Genomics Consortium (TBSGC)
Citation
Journal: 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.
#1: Journal: STRUCTURE / Year: 1996
Title: HUMAN DUTP PYROPHOSPHATASE: URACIL RECOGNITION BY A BETA HAIRPIN AND ACTIVE SITES FORMED BY THREE SEPARATE SUBUNITS
Authors: Mol, C.D. / Harris, J.M. / Mclntosh, E.M. / Tainer, J.A.
History
DepositionSep 13, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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)16,0653
Polymers15,8211
Non-polymers2442
Water2,432135
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)48,1969
Polymers47,4633
Non-polymers7336
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area10280 Å2
ΔGint-33 kcal/mol
Surface area16280 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)98.823, 98.823, 98.823
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-155-

TRS

21A-155-

TRS

31A-156-

TRS

41A-156-

TRS

51A-200-

HOH

61A-251-

HOH

DetailsThe biological assembly is a trimer that is generated by the following crystallographic symmetry operators -y+1, -z+1, x and z, -x+1, -y+1

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Components

#1: Protein DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE / dUTPase / dUTP pyrophosphatase


Mass: 15820.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv2697c / Production host: Escherichia coli (E. coli)
References: UniProt: P0A552, UniProt: P9WNS5*PLUS, dUTP diphosphatase
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.54 Å3/Da / Density % sol: 51.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG4000, EDTA, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
160 mg/mlprotein1drop
216 %(w/v)PEG40001reservoir
30.13 mMEDTA1reservoir
40.1 MTris-HCl1reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 23, 2002
RadiationMonochromator: Si (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→31.25 Å / Num. all: 11317 / Num. obs: 11317 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18 % / Biso Wilson estimate: 17.3 Å2 / Rsym value: 0.078 / Net I/σ(I): 62.7
Reflection shellResolution: 1.95→2.02 Å / Num. unique all: 1172 / Rsym value: 0.393 / % possible all: 100
Reflection
*PLUS
Num. obs: 11592 / Num. measured all: 208809 / Rmerge(I) obs: 0.078
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 13.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DUD

1dud


Resolution: 1.95→31.25 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1170 10.3 %RANDOM
Rwork0.197 ---
all0.1999 11317 --
obs0.197 11317 95.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.1896 Å2 / ksol: 0.366749 e/Å3
Displacement parametersBiso mean: 31.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error free: 0.26 Å / Luzzati sigma a free: 0.14 Å
Refinement stepCycle: LAST / Resolution: 1.95→31.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms985 0 8 135 1128
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_improper_angle_d0.83
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.258 202 10.9 %
Rwork0.231 1646 -
obs--95.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3TRS.PARAMTRS.TOP
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83

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