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- PDB-4xjc: dCTP deaminase-dUTPase from Bacillus halodurans -

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Basic information

Entry
Database: PDB / ID: 4xjc
TitledCTP deaminase-dUTPase from Bacillus halodurans
ComponentsDeoxycytidine triphosphate deaminase
KeywordsHYDROLASE / bifunctional / TTP binding / complex
Function / homology
Function and homology information


dCTP deaminase (dUMP-forming) / dCTP deaminase (dUMP-forming) activity / dUTP biosynthetic process / dCTP deaminase activity / dUMP biosynthetic process / nucleotide binding
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
DI(HYDROXYETHYL)ETHER / THYMIDINE-5'-TRIPHOSPHATE / dCTP deaminase, dUMP-forming
Similarity search - Component
Biological speciesBacillus halodurans C-125 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsOehlenschlaeger, C. / Loevgreen, M. / Willemoes, M. / Harris, P.
CitationJournal: Appl.Environ.Microbiol. / Year: 2015
Title: Bacillus halodurans Strain C125 Encodes and Synthesizes Enzymes from Both Known Pathways To Form dUMP Directly from Cytosine Deoxyribonucleotides.
Authors: Oehlenschlger, C.B. / Lvgreen, M.N. / Reinauer, E. / Lehtinen, E. / Pind, M.L. / Harris, P. / Martinussen, J. / Willemoes, M.
History
DepositionJan 8, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 10, 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 / 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deoxycytidine triphosphate deaminase
C: Deoxycytidine triphosphate deaminase
E: Deoxycytidine triphosphate deaminase
B: Deoxycytidine triphosphate deaminase
D: Deoxycytidine triphosphate deaminase
F: Deoxycytidine triphosphate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,64619
Polymers119,5016
Non-polymers3,14513
Water6,359353
1
A: Deoxycytidine triphosphate deaminase
C: Deoxycytidine triphosphate deaminase
E: Deoxycytidine triphosphate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,37610
Polymers59,7503
Non-polymers1,6267
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14480 Å2
ΔGint-103 kcal/mol
Surface area18690 Å2
MethodPISA
2
B: Deoxycytidine triphosphate deaminase
D: Deoxycytidine triphosphate deaminase
F: Deoxycytidine triphosphate deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2709
Polymers59,7503
Non-polymers1,5196
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13790 Å2
ΔGint-102 kcal/mol
Surface area18600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.720, 55.630, 95.600
Angle α, β, γ (deg.)90.00, 97.36, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13A
23B
14A
24D
15A
25F
16C
26E
17C
27B
18C
28D
19C
29F
110E
210B
111E
211D
112E
212F
113B
213D
114B
214F
115D
215F

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHEAA1 - 1771 - 177
21PHEPHECB1 - 1771 - 177
12PHEPHEAA1 - 1771 - 177
22PHEPHEEC1 - 1771 - 177
13PHEPHEAA1 - 1771 - 177
23PHEPHEBD1 - 1771 - 177
14PHEPHEAA1 - 1771 - 177
24PHEPHEDE1 - 1771 - 177
15LYSLYSAA1 - 1741 - 174
25LYSLYSFF1 - 1741 - 174
16PHEPHECB1 - 1771 - 177
26PHEPHEEC1 - 1771 - 177
17PHEPHECB1 - 1771 - 177
27PHEPHEBD1 - 1771 - 177
18PHEPHECB1 - 1771 - 177
28PHEPHEDE1 - 1771 - 177
19LYSLYSCB1 - 1741 - 174
29LYSLYSFF1 - 1741 - 174
110PHEPHEEC1 - 1771 - 177
210PHEPHEBD1 - 1771 - 177
111PHEPHEEC1 - 1771 - 177
211PHEPHEDE1 - 1771 - 177
112LYSLYSEC1 - 1741 - 174
212LYSLYSFF1 - 1741 - 174
113PHEPHEBD1 - 1771 - 177
213PHEPHEDE1 - 1771 - 177
114LYSLYSBD1 - 1741 - 174
214LYSLYSFF1 - 1741 - 174
115LYSLYSDE1 - 1741 - 174
215LYSLYSFF1 - 1741 - 174

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Deoxycytidine triphosphate deaminase / dCTP deaminase


Mass: 19916.785 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans C-125 (bacteria) / Gene: dcd, BH0368 / Production host: Bacillus halodurans C-125 (bacteria) / References: UniProt: Q9KFV3, dCTP deaminase
#2: Chemical
ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE


Mass: 482.168 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: Mg
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.35 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: 200 mM lithium citrate, 20% PEG4000 / PH range: 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.03796 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03796 Å / Relative weight: 1
ReflectionResolution: 2.35→95 Å / Num. obs: 40236 / % possible obs: 98.8 % / Redundancy: 3.27 % / Rmerge(I) obs: 0.164 / Net I/σ(I): 8.87
Reflection shellResolution: 2.35→2.64 Å / Rmerge(I) obs: 0.761

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QXX

2qxx


Resolution: 2.35→94.81 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.903 / SU B: 19.354 / SU ML: 0.239 / Cross valid method: THROUGHOUT / ESU R: 0.915 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24385 2013 5 %RANDOM
Rwork0.20716 ---
obs0.20901 38223 98.84 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.59 Å2
Baniso -1Baniso -2Baniso -3
1-1.97 Å20 Å21.29 Å2
2---2.73 Å2-0 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 2.35→94.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8359 0 187 353 8899
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0198729
X-RAY DIFFRACTIONr_bond_other_d0.0080.028366
X-RAY DIFFRACTIONr_angle_refined_deg1.6252.00111895
X-RAY DIFFRACTIONr_angle_other_deg1.41319301
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.39251047
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57224.075373
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.566151483
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0141554
X-RAY DIFFRACTIONr_chiral_restr0.0810.21360
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219546
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021888
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1921.5074209
X-RAY DIFFRACTIONr_mcbond_other1.1911.5074208
X-RAY DIFFRACTIONr_mcangle_it1.9812.2545249
X-RAY DIFFRACTIONr_mcangle_other1.9812.2545250
X-RAY DIFFRACTIONr_scbond_it1.6111.7644520
X-RAY DIFFRACTIONr_scbond_other1.611.7644520
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5952.5766647
X-RAY DIFFRACTIONr_long_range_B_refined5.18113.2199826
X-RAY DIFFRACTIONr_long_range_B_other5.14513.1039744
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A106910.08
12C106910.08
21A105750.09
22E105750.09
31A106830.07
32B106830.07
41A105840.09
42D105840.09
51A102250.08
52F102250.08
61C105670.09
62E105670.09
71C105380.09
72B105380.09
81C106570.1
82D106570.1
91C102220.09
92F102220.09
101E107100.08
102B107100.08
111E105510.09
112D105510.09
121E103850.07
122F103850.07
131B106590.08
132D106590.08
141B102970.07
142F102970.07
151D103450.08
152F103450.08
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 157 -
Rwork0.324 2624 -
obs--93.42 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5485-0.0686-0.32230.83080.04811.4688-0.0841-0.148-0.0483-0.02360.028-0.04990.22240.24910.05610.05780.06890.03130.30620.01460.026932.674-9.57518.062
21.4419-0.1611-0.40060.8812-0.35851.31570.0646-0.08690.2699-0.01460.0187-0.0386-0.09380.1669-0.08330.029-0.01880.03530.2583-0.04870.078627.88112.8118.057
31.2658-0.497-0.24041.23790.03931.4527-0.0221-0.04080.0195-0.01530.04750.11190.0878-0.099-0.02540.0213-0.00010.01380.26480.02160.03511.029-2.7220.914
40.89080.0241-0.21790.80270.0822.7346-0.05520.0445-0.10890.0476-0.01670.03690.2394-0.01050.07190.04210.00870.02770.2154-0.00980.0326.779-16.825-23.785
51.6177-0.2819-1.45141.54220.38552.50750.23350.35740.22110.038-0.14920.0991-0.3273-0.6276-0.08430.05180.08310.02140.4551-0.00790.10448.612-3.313-27.467
60.91850.0484-0.68390.91680.40542.42010.21950.05490.185-0.0076-0.03180.0722-0.62980.0643-0.18770.1785-0.0120.06680.25040.00740.047430.4374.812-29.416
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 177
2X-RAY DIFFRACTION2C1 - 177
3X-RAY DIFFRACTION3E1 - 177
4X-RAY DIFFRACTION4B1 - 177
5X-RAY DIFFRACTION5D1 - 177
6X-RAY DIFFRACTION6F1 - 174

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