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- PDB-2qlp: Bifunctional dCTP deaminase:dUTPase from Mycobacterium tuberculos... -

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Basic information

Entry
Database: PDB / ID: 2qlp
TitleBifunctional dCTP deaminase:dUTPase from Mycobacterium tuberculosis, apo form
ComponentsDeoxycytidine triphosphate deaminase
KeywordsHYDROLASE / distorted beta barrel / Nucleotide metabolism
Function / homology
Function and homology information


dCTP deaminase (dUMP-forming) / dCTP deaminase (dUMP-forming) activity / dUTP biosynthetic process / dCTP deaminase activity / dUMP biosynthetic process / dUTP diphosphatase activity / nucleobase-containing small molecule interconversion / nucleotide binding
Similarity search - Function
dCTP deaminase / dCTP deaminase-like / 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
dCTP deaminase, dUMP-forming / dCTP deaminase, dUMP-forming
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsChristophersen, S. / Harris, P. / Willemoes, M.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Mechanism of dTTP inhibition of the bifunctional dCTP deaminase:dUTPase encoded by Mycobacterium tuberculosis
Authors: Helt, S.S. / Thymark, M. / Harris, P. / Aagaard, C. / Dietrich, J. / Larsen, S. / Willemoes, M.
History
DepositionJul 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 21, 2024Group: 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 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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: Deoxycytidine triphosphate deaminase
B: Deoxycytidine triphosphate deaminase
C: Deoxycytidine triphosphate deaminase
D: Deoxycytidine triphosphate deaminase
E: Deoxycytidine triphosphate deaminase
F: Deoxycytidine triphosphate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,67113
Polymers106,0036
Non-polymers1,6687
Water2,162120
1
A: Deoxycytidine triphosphate deaminase
B: Deoxycytidine triphosphate deaminase
C: Deoxycytidine triphosphate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9547
Polymers53,0013
Non-polymers9534
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10160 Å2
MethodPISA
2
D: Deoxycytidine triphosphate deaminase
E: Deoxycytidine triphosphate deaminase
F: Deoxycytidine triphosphate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7166
Polymers53,0013
Non-polymers7153
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.800, 96.700, 78.000
Angle α, β, γ (deg.)90.000, 97.700, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71A
81B
91C
101D
111E
121F

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETLYSLYSAA1 - 551 - 55
21METMETLYSLYSBB1 - 551 - 55
31METMETLYSLYSCC1 - 551 - 55
41METMETLYSLYSDD1 - 551 - 55
51METMETLYSLYSEE1 - 551 - 55
61METMETLYSLYSFF1 - 551 - 55
72HISHISSERSERAA75 - 15875 - 158
82HISHISSERSERBB75 - 15875 - 158
92HISHISSERSERCC75 - 15875 - 158
102HISHISSERSERDD75 - 15875 - 158
112HISHISSERSEREE75 - 15875 - 158
122HISHISSERSERFF75 - 15875 - 158

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Components

#1: Protein
Deoxycytidine triphosphate deaminase / dCTP deaminase


Mass: 17667.109 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: dcd / Plasmid: pTBdcd7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O07247, UniProt: P9WP17*PLUS, dCTP deaminase
#2: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.21 Å3/Da / Density % sol: 44.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.9mg/ml enzyme in 50mM HEPES pH 6.8 Reservoir: 20% PEG 8K, 50mM MgCl2, 100mM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 22, 2007
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.47→20 Å / Num. all: 32512 / Num. obs: 32512 / % possible obs: 99.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 28.425 Å2 / Rmerge(I) obs: 0.193 / Net I/σ(I): 6.81
Reflection shellHighest resolution: 2.47 Å / Rmerge(I) obs: 0.551 / Mean I/σ(I) obs: 2.2 / Num. measured obs: 33612 / Num. unique all: 9296 / % possible all: 99

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.59 Å19.91 Å
Translation2.59 Å19.91 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
MxCuBEdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.47→19.9 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.827 / SU B: 14.383 / SU ML: 0.319 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.928 / ESU R Free: 0.366 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.295 1626 5 %RANDOM
Rwork0.228 ---
all0.232 32512 --
obs0.232 32512 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.419 Å2
Baniso -1Baniso -2Baniso -3
1-1.13 Å20 Å2-3 Å2
2---1.41 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 2.47→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7362 0 73 120 7555
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227581
X-RAY DIFFRACTIONr_angle_refined_deg1.4972.00110277
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4215950
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.01723.918319
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.352151260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0521554
X-RAY DIFFRACTIONr_chiral_restr0.1130.21196
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025654
X-RAY DIFFRACTIONr_nbd_refined0.2610.32997
X-RAY DIFFRACTIONr_nbtor_refined0.3280.54968
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2210.5504
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2850.332
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1120.52
X-RAY DIFFRACTIONr_mcbond_it0.73424857
X-RAY DIFFRACTIONr_mcangle_it1.25737711
X-RAY DIFFRACTIONr_scbond_it0.72222939
X-RAY DIFFRACTIONr_scangle_it1.12732566
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A556TIGHT POSITIONAL0.050.05
2B556TIGHT POSITIONAL0.060.05
3C556TIGHT POSITIONAL0.060.05
4D556TIGHT POSITIONAL0.050.05
5E556TIGHT POSITIONAL0.050.05
6F556TIGHT POSITIONAL0.050.05
1A511MEDIUM POSITIONAL0.460.5
2B511MEDIUM POSITIONAL0.480.5
3C511MEDIUM POSITIONAL0.540.5
4D511MEDIUM POSITIONAL0.40.5
5E511MEDIUM POSITIONAL0.390.5
6F511MEDIUM POSITIONAL0.480.5
1A556TIGHT THERMAL0.10.5
2B556TIGHT THERMAL0.10.5
3C556TIGHT THERMAL0.090.5
4D556TIGHT THERMAL0.10.5
5E556TIGHT THERMAL0.090.5
6F556TIGHT THERMAL0.10.5
1A511MEDIUM THERMAL0.522
2B511MEDIUM THERMAL0.562
3C511MEDIUM THERMAL0.572
4D511MEDIUM THERMAL0.572
5E511MEDIUM THERMAL0.492
6F511MEDIUM THERMAL0.582
LS refinement shellResolution: 2.47→2.533 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 94 -
Rwork0.345 1791 -
obs-1885 100 %

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