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- PDB-1ogh: Structure of the bifunctional dCTP deaminase-dUTPase from Methano... -

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Basic information

Entry
Database: PDB / ID: 1ogh
TitleStructure of the bifunctional dCTP deaminase-dUTPase from Methanocaldococcus jannaschii
ComponentsBIFUNCTIONAL DEAMINASE/DIPHOSPHATASE
KeywordsHYDROLASE / BIFUNCTIONAL ENZYME / NUCLEOTIDE METABOLISM / DCTP DEAMINASE / DUTPASE / HOMOTRIMER
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, 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 / SIRAS / Resolution: 1.88 Å
AuthorsJohansson, E. / Bjornberg, O. / Nyman, P.O. / Larsen, S.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: Structure of the Bifunctional Dctp Deaminase-Dutpase from Methanocaldococcus Jannaschii and its Relation to Other Homotrimeric Dutpases
Authors: Johansson, E. / Bjornberg, O. / Nyman, P.O. / Larsen, S.
#1: Journal: J.Biol.Chem. / Year: 2003
Title: A Bifunctional Dctp Deaminase-Dutp Nucleotidohydrolase from the Hyperthermophilic Archaeon Methanocaldococcus Jannaschii
Authors: Bjornberg, O. / Neuhard, J. / Nyman, P.
History
DepositionMay 2, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2003Provider: 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 1.4Mar 6, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / pdbx_struct_special_symmetry / Item: _exptl_crystal_grow.method
Revision 1.5May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BIFUNCTIONAL DEAMINASE/DIPHOSPHATASE
B: BIFUNCTIONAL DEAMINASE/DIPHOSPHATASE


Theoretical massNumber of molelcules
Total (without water)46,9242
Polymers46,9242
Non-polymers00
Water7,170398
1
A: BIFUNCTIONAL DEAMINASE/DIPHOSPHATASE

A: BIFUNCTIONAL DEAMINASE/DIPHOSPHATASE

A: BIFUNCTIONAL DEAMINASE/DIPHOSPHATASE


Theoretical massNumber of molelcules
Total (without water)70,3863
Polymers70,3863
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
MethodPQS
2
B: BIFUNCTIONAL DEAMINASE/DIPHOSPHATASE

B: BIFUNCTIONAL DEAMINASE/DIPHOSPHATASE

B: BIFUNCTIONAL DEAMINASE/DIPHOSPHATASE


Theoretical massNumber of molelcules
Total (without water)70,3863
Polymers70,3863
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z+1/2,-x+1/2,-y1
crystal symmetry operation12_554-y+1/2,-z,x-1/21
MethodPQS
Unit cell
Length a, b, c (Å)111.060, 111.060, 111.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-2106-

HOH

21A-2156-

HOH

31A-2157-

HOH

41B-2116-

HOH

51B-2117-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1
2114B1
1214A3 - 4
2214B3 - 4
1316A6
2316B6
1414A7 - 8
2414B7 - 8
1516A9
2516B9
1614A10 - 19
2614B10 - 19
1716A20
2716B20
1814A21 - 22
2814B21 - 22
1916A23 - 25
2916B23 - 25
11014A26 - 40
21014B26 - 40
11116A42
21116B42
11216A44
21216B44
11315A45 - 47
21315B45 - 47
11416A48
21416B48
11514A49 - 50
21514B49 - 50
11615A52
21615B52
11716A53
21716B53
11815A54 - 55
21815B54 - 55
11914A57
21914B57
12016A58 - 59
22016B58 - 59
12114A60 - 61
22114B60 - 61
12216A62 - 63
22216B62 - 63
12314A64 - 72
22314B64 - 72
12415A73
22415B73
12514A74 - 86
22514B74 - 86
12616A87
22616B87
12714A88 - 89
22714B88 - 89
12814A91 - 95
22814B91 - 95
12914A97 - 121
22914B97 - 121
13016A122
23016B122
13114A123 - 125
23114B123 - 125
13214A127 - 150
23214B127 - 150
13316A151
23316B151
13414A152 - 173
23414B152 - 173
13514A300 - 395
23514B300 - 395

NCS oper: (Code: given
Matrix: (0.7778, 0.5405, -0.3209), (-0.5389, 0.3107, -0.783), (-0.3235, 0.7819, 0.5329)
Vector: 12.2501, 43.8262, -42.998)

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Components

#1: Protein BIFUNCTIONAL DEAMINASE/DIPHOSPHATASE / MJDCD-DUT / DCD/DUT / (INCLUDES\: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE / (DCTP DEAMINASE) / ...MJDCD-DUT / DCD/DUT / (INCLUDES\: DEOXYCYTIDINE TRIPHOSPHATE DEAMINASE / (DCTP DEAMINASE) / DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE / (DUTPASE / DUTP PYROPHOSPHATASE))


Mass: 23461.854 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOCALDOCOCCUS JANNASCHII (archaea)
Plasmid: PET3A/MJ0430 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q57872, dCTP deaminase, dUTP diphosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE PROTEIN IS A BIFUNCTIONAL ENZYME THAT CATALYZES TWO CONSECUTIVE REACTIONS TO PRODUCE DUMP FROM ...THE PROTEIN IS A BIFUNCTIONAL ENZYME THAT CATALYZES TWO CONSECUTIVE REACTIONS TO PRODUCE DUMP FROM DCTP IN A TWO STEP REACTION. THE FIRST REACTION STEP IS A DEAMINATION STEP THAT PRODUCES DUTP FROM DCTP. IN THE SECOND LEG, DUTP IS DEPHOSPHORYLATED TO GENERATE DUMP. MEMBER OF THE DE NOVO THYMIDYLATE SYNTHESIS PATHWAY.

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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: 2.44 Å3/Da / Density % sol: 50 %
Crystal growMethod: vapor diffusion / pH: 8.5
Details: 3MG/ML PROTEIN VAPOUR DIFFUSION WITH MOTHER LIQUOR: 5% PEG8000, 0.1 M TRIS-HCL, PH8.5, pH 8.50
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
13 mg/mlprotein1drop
220 mMTris-HCl1droppH8.5
35 %PEG80001reservoir
40.1 MTris-HCl1reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.098
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 18, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.098 Å / Relative weight: 1
ReflectionResolution: 1.88→45 Å / Num. obs: 37385 / % possible obs: 100 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 52
Reflection shellResolution: 1.88→1.92 Å / Rmerge(I) obs: 0.136 / Mean I/σ(I) obs: 21 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 1.88 Å / Lowest resolution: 45 Å / % possible obs: 100 % / Num. measured all: 417089 / Rmerge(I) obs: 0.042
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.136 / Mean I/σ(I) obs: 21

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.88→19.65 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.009 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.THE FINAL 29 AND 23 RESIDUES FOR CHAINS A AND B RESPECTIVELY WERE NOT SEEN IN THE ELECTRON DENSITY MAP. THE FUNCTIONAL UNIT OF THE MODEL IS ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.THE FINAL 29 AND 23 RESIDUES FOR CHAINS A AND B RESPECTIVELY WERE NOT SEEN IN THE ELECTRON DENSITY MAP. THE FUNCTIONAL UNIT OF THE MODEL IS A HOMOTRIMER. THE TWO CHAINS EACH GIVE RISE TO A HOMOTRIMER BY MEANS OF
RfactorNum. reflection% reflectionSelection details
Rfree0.184 1861 5 %RANDOM
Rwork0.147 ---
obs0.148 35449 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.66 Å2
Refinement stepCycle: LAST / Resolution: 1.88→19.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2879 0 0 398 3277
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223020
X-RAY DIFFRACTIONr_bond_other_d0.0020.022772
X-RAY DIFFRACTIONr_angle_refined_deg1.6371.9694095
X-RAY DIFFRACTIONr_angle_other_deg0.92636491
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8165354
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1760.2472
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023249
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02600
X-RAY DIFFRACTIONr_nbd_refined0.1930.2498
X-RAY DIFFRACTIONr_nbd_other0.2430.23113
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0860.21874
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2273
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3630.241
X-RAY DIFFRACTIONr_symmetry_vdw_other0.310.2222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2950.284
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.021.51785
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.93622942
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.94731235
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8874.51153
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
LS refinement shellResolution: 1.88→1.93 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.219 134
Rwork0.158 2573
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rwork: 0.146
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.018
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.63
LS refinement shell
*PLUS
Rfactor Rfree: 0.22 / Rfactor Rwork: 0.158

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