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- PDB-2hxb: dCTP deaminase-dUTPase from Methanocaldococcus jannaschii -

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Basic information

Entry
Database: PDB / ID: 2hxb
TitledCTP deaminase-dUTPase from Methanocaldococcus jannaschii
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 / nucleobase-containing small molecule interconversion / 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
dCTP deaminase, dUMP-forming
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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 1.2May 23, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Oct 25, 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_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: dCTP deaminase, dUMP-forming


Theoretical massNumber of molelcules
Total (without water)23,4621
Polymers23,4621
Non-polymers00
Water82946
1
A: dCTP deaminase, dUMP-forming

A: dCTP deaminase, dUMP-forming

A: dCTP deaminase, dUMP-forming


Theoretical massNumber of molelcules
Total (without water)70,3863
Polymers70,3863
Non-polymers00
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 area9790 Å2
ΔGint-61 kcal/mol
Surface area21220 Å2
MethodPISA
2
A: dCTP deaminase, dUMP-forming
x 6


Theoretical massNumber of molelcules
Total (without water)140,7716
Polymers140,7716
Non-polymers00
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 area23230 Å2
ΔGint-131 kcal/mol
Surface area38780 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)170.896, 170.896, 170.896
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-206-

HOH

21A-233-

HOH

31A-249-

HOH

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Components

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


Mass: 23461.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: dcd / Plasmid: pET3a / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 7.5
Details: 30 % PEG400, 0.2M calcium chloride dihydrate, 0.1M HEPES, 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: 1.007 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 21, 2003
RadiationMonochromator: Monochromator 0.900 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.007 Å / Relative weight: 1
ReflectionResolution: 2.55→30 Å / Num. obs: 14069 / % possible obs: 100 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.0127 / Net I/σ(I): 19.4
Reflection shellResolution: 2.55→2.61 Å / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 4.8 / Num. unique all: 14069 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
AMoREphasing
REFMAC5.1.24refinement
PDB_EXTRACT2data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OGH

1ogh


Resolution: 2.55→25 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.096 / SU ML: 0.113 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.198 708 5 %RANDOM
Rwork0.185 ---
all0.2 ---
obs-14059 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.602 Å2
Refinement stepCycle: LAST / Resolution: 2.55→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1414 0 0 46 1460
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221442
X-RAY DIFFRACTIONr_bond_other_d0.0020.021316
X-RAY DIFFRACTIONr_angle_refined_deg1.621.9711951
X-RAY DIFFRACTIONr_angle_other_deg0.84733078
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9175174
X-RAY DIFFRACTIONr_chiral_restr0.0930.2221
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021573
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02283
X-RAY DIFFRACTIONr_nbd_refined0.1870.2218
X-RAY DIFFRACTIONr_nbd_other0.2370.21408
X-RAY DIFFRACTIONr_nbtor_other0.0870.2894
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.243
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1190.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2960.287
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.217
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.308 47
Rwork0.254 966
obs-1013

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