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- PDB-2hxd: Bifunctional dCTP deaminase-dUTPase mutant enzyme variant E145A f... -

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Basic information

Entry
Database: PDB / ID: 2hxd
TitleBifunctional dCTP deaminase-dUTPase mutant enzyme variant E145A from Methanocaldococcus jannaschii in complex with alpha,beta-imido dUTP and magnesium
ComponentsdCTP deaminase, dUMP-forming
KeywordsHYDROLASE / beta barrel
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 / 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
2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE / dCTP deaminase, dUMP-forming
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsBynck, J.H. / Johansson, E.
CitationJournal: To be Published
Title: Structural evidence for a concerted Bifunctionality in dCTP deaminase-dUTPase from Methanocaldococcus jannaschii
Authors: Bynck, J.H. / Willemoes, M. / Larsen, S. / Johansson, E.
History
DepositionAug 3, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: dCTP deaminase, dUMP-forming
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8953
Polymers23,4041
Non-polymers4912
Water2,180121
1
A: dCTP deaminase, dUMP-forming
hetero molecules

A: dCTP deaminase, dUMP-forming
hetero molecules

A: dCTP deaminase, dUMP-forming
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6869
Polymers70,2113
Non-polymers1,4746
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation11_566y,-z+1,-x+11
Buried area14600 Å2
ΔGint-89 kcal/mol
Surface area21370 Å2
MethodPISA
2
A: dCTP deaminase, dUMP-forming
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)143,37218
Polymers140,4236
Non-polymers2,94912
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation11_566y,-z+1,-x+11
crystal symmetry operation38_556-y+1/2,-x+1/2,-z+3/21
crystal symmetry operation42_545-x+1/2,z-1/2,y+1/21
crystal symmetry operation46_455z-1/2,-y+1/2,x+1/21
Buried area32370 Å2
ΔGint-184 kcal/mol
Surface area39580 Å2
MethodPISA
3
A: dCTP deaminase, dUMP-forming
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)573,48772
Polymers561,69224
Non-polymers11,79548
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_656-y+1,z,-x+11
crystal symmetry operation11_566y,-z+1,-x+11
crystal symmetry operation12_665-y+1,-z+1,x1
crystal symmetry operation13_556y,x,-z+11
crystal symmetry operation14_666-y+1,-x+1,-z+11
crystal symmetry operation15_565y,-x+1,z1
crystal symmetry operation16_655-y+1,x,z1
crystal symmetry operation17_556x,z,-y+11
crystal symmetry operation18_655-x+1,z,y1
crystal symmetry operation19_666-x+1,-z+1,-y+11
crystal symmetry operation20_565x,-z+1,y1
crystal symmetry operation21_556z,y,-x+11
crystal symmetry operation22_565z,-y+1,x1
crystal symmetry operation23_655-z+1,y,x1
crystal symmetry operation24_666-z+1,-y+1,-x+11
MethodPQS
Unit cell
Length a, b, c (Å)171.513, 171.513, 171.513
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number211
Space group name H-MI432
Components on special symmetry positions
IDModelComponents
11A-289-

HOH

21A-291-

HOH

31A-293-

HOH

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Components

#1: Protein dCTP deaminase, dUMP-forming / / Bifunctional deaminase/diphosphatase / MjDCD-DUT / DCD/DUT


Mass: 23403.818 Da / Num. of mol.: 1 / Mutation: E145A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: dcd / Plasmid: pET-3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q57872, dCTP deaminase (dUMP-forming)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-DUP / 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 4.44 Å3/Da / Density % sol: 72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.2
Details: 20 % PEG3350, 0.2M di-potassium hydrogen phosphate, pH 9.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 23, 2005
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. all: 18566 / Num. obs: 18566 / % possible obs: 100 % / Redundancy: 4.36 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 14.4
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 3 / Num. unique all: 2746 / % possible all: 98.9

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
DNAdata collection
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2HXB

2hxb


Resolution: 2.3→24.75 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.773 / SU ML: 0.114 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.221 924 5 %RANDOM
Rwork0.178 ---
all0.18 18560 --
obs-17636 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.131 Å2
Refinement stepCycle: LAST / Resolution: 2.3→24.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1606 0 29 121 1756
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221668
X-RAY DIFFRACTIONr_bond_other_d0.0010.021504
X-RAY DIFFRACTIONr_angle_refined_deg1.8441.9972261
X-RAY DIFFRACTIONr_angle_other_deg0.94233520
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4965198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.88824.79573
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.32815301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.96156
X-RAY DIFFRACTIONr_chiral_restr0.1010.2252
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021794
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02326
X-RAY DIFFRACTIONr_nbd_refined0.1950.2287
X-RAY DIFFRACTIONr_nbd_other0.1820.21464
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2782
X-RAY DIFFRACTIONr_nbtor_other0.0880.2996
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.295
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2480.232
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3020.2116
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.230
X-RAY DIFFRACTIONr_mcbond_it1.3761.51271
X-RAY DIFFRACTIONr_mcbond_other0.1971.5405
X-RAY DIFFRACTIONr_mcangle_it1.59121611
X-RAY DIFFRACTIONr_scbond_it2.6433822
X-RAY DIFFRACTIONr_scangle_it3.7394.5650
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 78 -
Rwork0.264 1308 -
obs-1386 100 %

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