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- PDB-2v9x: E138D variant of Escherichia coli dCTP deaminase in complex with dUTP -

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Basic information

Entry
Database: PDB / ID: 2v9x
TitleE138D variant of Escherichia coli dCTP deaminase in complex with dUTP
ComponentsDEOXYCYTIDINE TRIPHOSPHATE DEAMINASE
KeywordsHYDROLASE / DUTPASE / DCTP DEAMINASE / NUCLEOTIDE METABOLISM
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 / dCTP deaminase-like / Deoxyuridine triphosphatase (dUTPase) / Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A / 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 / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsThymark, M. / Johansson, E. / Larsen, S. / Willemoes, M.
CitationJournal: Arch.Biochem.Biophys. / Year: 2008
Title: Mutational Analysis of the Nucleotide Binding Site of Escherichia Coli Dctp Deaminase.
Authors: Thymark, M. / Johansson, E. / Larsen, S. / Willemoes, M.
History
DepositionAug 28, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_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_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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
G: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE
H: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE
I: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE
J: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE
K: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE
L: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,44040
Polymers255,14712
Non-polymers6,29428
Water8,287460
1
A: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE
B: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE
C: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE
J: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE
K: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE
L: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,72020
Polymers127,5736
Non-polymers3,14714
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30230 Å2
ΔGint-84 kcal/mol
Surface area43650 Å2
MethodPQS
2
D: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE
E: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE
F: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE
G: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE
H: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE
I: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,72020
Polymers127,5736
Non-polymers3,14714
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30620 Å2
ΔGint-121.3 kcal/mol
Surface area44030 Å2
MethodPQS
Unit cell
Length a, b, c (Å)94.187, 71.301, 319.916
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101K

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 1 / Auth seq-ID: 1 - 193 / Label seq-ID: 1 - 193

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH
9II
10KK

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Components

#1: Protein
DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE / DCTP DEAMINASE


Mass: 21262.230 Da / Num. of mol.: 12 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P28248, dCTP deaminase
#2: Chemical
ChemComp-DUT / DEOXYURIDINE-5'-TRIPHOSPHATE


Mass: 468.142 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C9H15N2O14P3
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 460 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 138 TO ASP ENGINEERED RESIDUE IN CHAIN B, GLU 138 TO ASP ...ENGINEERED RESIDUE IN CHAIN A, GLU 138 TO ASP ENGINEERED RESIDUE IN CHAIN B, GLU 138 TO ASP ENGINEERED RESIDUE IN CHAIN C, GLU 138 TO ASP ENGINEERED RESIDUE IN CHAIN D, GLU 138 TO ASP ENGINEERED RESIDUE IN CHAIN E, GLU 138 TO ASP ENGINEERED RESIDUE IN CHAIN F, GLU 138 TO ASP ENGINEERED RESIDUE IN CHAIN G, GLU 138 TO ASP ENGINEERED RESIDUE IN CHAIN H, GLU 138 TO ASP ENGINEERED RESIDUE IN CHAIN I, GLU 138 TO ASP ENGINEERED RESIDUE IN CHAIN J, GLU 138 TO ASP ENGINEERED RESIDUE IN CHAIN K, GLU 138 TO ASP ENGINEERED RESIDUE IN CHAIN L, GLU 138 TO ASP

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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: 2.1 Å3/Da / Density % sol: 41 % / Description: NONE
Crystal growpH: 7.5 / Details: 27.5 %PEG 400, 50 MM MGSO4, 0.1 M HEPES, PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 108216 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 15.5
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.03 / Mean I/σ(I) obs: 3.2 / % possible all: 84.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XS1

1xs1


Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.918 / SU B: 6.073 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.373 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.239 5341 5 %RANDOM
Rwork0.203 ---
obs0.205 101282 96.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.61 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å20 Å20 Å2
2--1.01 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17531 0 368 460 18359
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02218263
X-RAY DIFFRACTIONr_bond_other_d0.0030.0216958
X-RAY DIFFRACTIONr_angle_refined_deg1.7432.00424862
X-RAY DIFFRACTIONr_angle_other_deg1.007339135
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.652252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.57122.383814
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.773152934
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6215209
X-RAY DIFFRACTIONr_chiral_restr0.0940.22730
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0220232
X-RAY DIFFRACTIONr_gen_planes_other0.0040.023789
X-RAY DIFFRACTIONr_nbd_refined0.2110.22984
X-RAY DIFFRACTIONr_nbd_other0.2050.216265
X-RAY DIFFRACTIONr_nbtor_refined0.1740.28583
X-RAY DIFFRACTIONr_nbtor_other0.0890.211192
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.2641
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.550.2103
X-RAY DIFFRACTIONr_symmetry_vdw_other0.5260.2240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2550.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.391.511940
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.014218057
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.94937597
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.6524.56805
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2929 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.040.05
2Btight positional0.050.05
3Ctight positional0.060.05
4Dtight positional0.040.05
5Etight positional0.050.05
6Ftight positional0.050.05
7Gtight positional0.040.05
8Htight positional0.040.05
9Itight positional0.050.05
10Ktight positional0.050.05
1Atight thermal0.160.5
2Btight thermal0.150.5
3Ctight thermal0.170.5
4Dtight thermal0.150.5
5Etight thermal0.150.5
6Ftight thermal0.140.5
7Gtight thermal0.170.5
8Htight thermal0.140.5
9Itight thermal0.150.5
10Ktight thermal0.180.5
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.286 351
Rwork0.245 6462

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