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- PDB-2qxx: Bifunctional dCTP deaminase: dUTPase from Mycobacterium tuberculo... -

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Basic information

Entry
Database: PDB / ID: 2qxx
TitleBifunctional dCTP deaminase: dUTPase from Mycobacterium tuberculosis in complex with dTTP
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 / nucleobase-containing small molecule interconversion / dUTP diphosphatase activity / nucleotide binding
Similarity search - Function
dCTP deaminase / 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
THYMIDINE-5'-TRIPHOSPHATE / dCTP deaminase, dUMP-forming / dCTP deaminase, dUMP-forming
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChristophersen, S. / Harris, P. / Willemoes, M.
CitationJournal: J.Mol.Biol. / Year: 2008
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
DepositionAug 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 1.2Aug 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.pdbx_dist_value / _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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_seq_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

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Assembly

Deposited unit
A: Deoxycytidine triphosphate deaminase
B: Deoxycytidine triphosphate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5119
Polymers41,7832
Non-polymers1,7287
Water3,045169
1
A: Deoxycytidine triphosphate deaminase
hetero molecules

A: Deoxycytidine triphosphate deaminase
hetero molecules

A: Deoxycytidine triphosphate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,90912
Polymers62,6753
Non-polymers2,2349
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555z,x,y1
crystal symmetry operation3_555y,z,x1
Buried area15550 Å2
MethodPISA
2
B: Deoxycytidine triphosphate deaminase
hetero molecules

B: Deoxycytidine triphosphate deaminase
hetero molecules

B: Deoxycytidine triphosphate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,62415
Polymers62,6753
Non-polymers2,94912
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555z,x,y1
crystal symmetry operation3_555y,z,x1
Buried area15680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.640, 82.640, 82.640
Angle α, β, γ (deg.)70.750, 70.750, 70.750
Int Tables number155
Space group name H-MR32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETHISHISAA1 - 1121 - 112
21METMETHISHISBB1 - 1121 - 112
32ILEILESERSERAA118 - 180118 - 180
42ILEILESERSERBB118 - 180118 - 180
53TTPTTPMGMGAD - C201 - 202
63TTPTTPMGMGBG - F201 - 202

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Components

#1: Protein Deoxycytidine triphosphate deaminase / dCTP deaminase


Mass: 20891.604 Da / Num. of mol.: 2
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE


Mass: 482.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


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


Mass: 18.015 Da / Num. of mol.: 169 / 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: 1.94 Å3/Da / Density % sol: 36.72 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.9 mg/ml enzyme in 20 mM MgCl2, 5mM dTTP, 50mM HEPES pH 6.8 reservoir solution: 45% PEG 400, 200mM MgCl2, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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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: Nov 17, 2006
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→19.6 Å / Num. all: 22235 / Num. obs: 22235 / % possible obs: 98.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.025 Å2 / Rmerge(I) obs: 0.159 / Net I/σ(I): 15.01
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 4.5 / Num. measured obs: 33274 / Num. unique all: 2973 / % possible all: 97.8

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.49 Å19.51 Å
Translation2.49 Å19.51 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
Starting model: PDB entry 1XS1

1xs1


Resolution: 2→19.58 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.257 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.201 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1112 5 %RANDOM
Rwork0.161 ---
all0.164 22234 --
obs0.164 22234 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: 16.975 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å2-1.08 Å2-1.08 Å2
2--0.71 Å2-1.08 Å2
3---0.71 Å2
Refinement stepCycle: LAST / Resolution: 2→19.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2924 0 84 169 3177
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0213071
X-RAY DIFFRACTIONr_angle_refined_deg1.3782.0134170
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9535376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.76523.182132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.34815494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6031526
X-RAY DIFFRACTIONr_chiral_restr0.0870.2460
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022308
X-RAY DIFFRACTIONr_nbd_refined0.2270.31166
X-RAY DIFFRACTIONr_nbtor_refined0.320.52060
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.220.5341
X-RAY DIFFRACTIONr_metal_ion_refined0.0090.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.3179
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2380.568
X-RAY DIFFRACTIONr_mcbond_it2.0741921
X-RAY DIFFRACTIONr_mcangle_it2.99563040
X-RAY DIFFRACTIONr_scbond_it2.43441263
X-RAY DIFFRACTIONr_scangle_it3.29961130
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1377 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.190.5
MEDIUM THERMAL0.872
LS refinement shellResolution: 2→2.043 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 81 -
Rwork0.206 1535 -
obs-1616 100 %

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