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- PDB-1xs1: dCTP deaminase from Escherichia coli in complex with dUTP -

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Basic information

Entry
Database: PDB / ID: 1xs1
TitledCTP deaminase from Escherichia coli in complex with dUTP
ComponentsDeoxycytidine triphosphate deaminase
KeywordsHYDROLASE / dCTP deaminase / nucleotide metabolism / trimer
Function / homology
Function and homology information


dCTP deaminase / dUTP biosynthetic process / dCTP deaminase activity / dUMP biosynthetic process / nucleobase-containing small molecule interconversion / dTTP biosynthetic process / protein homotrimerization / response to radiation / nucleotide binding / protein-containing complex ...dCTP deaminase / dUTP biosynthetic process / dCTP deaminase activity / dUMP biosynthetic process / nucleobase-containing small molecule interconversion / dTTP biosynthetic process / protein homotrimerization / response to radiation / nucleotide binding / protein-containing complex / identical protein binding / cytosol
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
DEOXYURIDINE-5'-TRIPHOSPHATE / dCTP deaminase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsJohansson, E. / Fano, M. / Bynck, J.H. / Neuhard, J. / Larsen, S. / Sigurskjold, B.W. / Christensen, U. / Willemoes, M.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structures of dCTP deaminase from Escherichia coli with bound substrate and product: reaction mechanism and determinants of mono- and bifunctionality for a family of enzymes
Authors: Johansson, E. / Fano, M. / Bynck, J.H. / Neuhard, J. / Larsen, S. / Sigurskjold, B.W. / Christensen, U. / Willemoes, M.
History
DepositionOct 18, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Data collection / Refinement description / Category: diffrn_source / software
Item: _diffrn_source.pdbx_synchrotron_site / _software.classification / _software.name
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_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_auth_seq_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_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_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.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_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)130,61218
Polymers127,6586
Non-polymers2,95512
Water7,692427
1
A: Deoxycytidine triphosphate deaminase
B: Deoxycytidine triphosphate deaminase
C: Deoxycytidine triphosphate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3069
Polymers63,8293
Non-polymers1,4776
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14450 Å2
ΔGint-84 kcal/mol
Surface area19690 Å2
MethodPISA
2
D: Deoxycytidine triphosphate deaminase
E: Deoxycytidine triphosphate deaminase
F: Deoxycytidine triphosphate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3069
Polymers63,8293
Non-polymers1,4776
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14540 Å2
ΔGint-81 kcal/mol
Surface area19640 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33230 Å2
ΔGint-187 kcal/mol
Surface area35090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.035, 97.461, 95.475
Angle α, β, γ (deg.)90.00, 109.23, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a trimer and the asymmetric unit contains two such trimers. The first trimer is built from chain A, B and C and the second trimer is built from chains D, E and F

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Components

#1: Protein
Deoxycytidine triphosphate deaminase / dCTP deaminase


Mass: 21276.256 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dcd / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P28248, dCTP deaminase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-DUT / DEOXYURIDINE-5'-TRIPHOSPHATE


Mass: 468.142 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H15N2O14P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / 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: 2.18 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 400, magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.087 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 14, 2003
RadiationMonochromator: Single asymmetrically cut Si(111) crystal with horizontal diffraction plane. The crystal is bendable for horizontal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.087 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. all: 335111 / Num. obs: 100803 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.036
Reflection shellResolution: 1.8→1.84 Å / Rsym value: 0.238 / % possible all: 0.826

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
MAR345data collection
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.8→25 Å / Num. parameters: 38488 / Num. restraintsaints: 66686 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: this is a twinned structure. The twinning operator is (h,k,l) -> (h,k,-h-l) and the twinning fraction is 0.47. The R-factor is 16.44% and the R-free is 19.51% when this twinning operator is ...Details: this is a twinned structure. The twinning operator is (h,k,l) -> (h,k,-h-l) and the twinning fraction is 0.47. The R-factor is 16.44% and the R-free is 19.51% when this twinning operator is used. For F>4SIG(F) the corresponding values are 16.08% and 19.12%, respectively.
RfactorNum. reflection% reflectionSelection details
Rfree0.1951 4789 5.3 %RANDOM
Rwork0.1644 ---
obs0.1644 85935 90.1 %-
all-90724 --
Refine analyzeNum. disordered residues: 10 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 9577
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9020 0 174 427 9621
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.021
X-RAY DIFFRACTIONs_similar_dist0.045
X-RAY DIFFRACTIONs_from_restr_planes0.028
X-RAY DIFFRACTIONs_zero_chiral_vol0.033
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.04
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.006
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.058
X-RAY DIFFRACTIONs_approx_iso_adps0

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