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- PDB-1pkh: STRUCTURAL BASIS FOR RECOGNITION AND CATALYSIS BY THE BIFUNCTIONA... -

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Basic information

Entry
Database: PDB / ID: 1pkh
TitleSTRUCTURAL BASIS FOR RECOGNITION AND CATALYSIS BY THE BIFUNCTIONAL DCTP DEAMINASE AND DUTPASE FROM METHANOCOCCUS JANNASCHII
ComponentsBifunctional deaminase/diphosphatase
KeywordsHYDROLASE / DCTP DEAMINASE / DUTPASE / DCD-DUT / MJ0430 / DCTP / DUTP
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
dCTP deaminase, dUMP-forming
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.42 Å
AuthorsHuffman, J.L. / Li, H. / White, R.H. / Tainer, J.A.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Structural basis for recognition and catalysis by the bifunctional dCTP deaminase and dUTPase from Methanococcus jannaschii
Authors: Huffman, J.L. / Li, H. / White, R.H. / Tainer, J.A.
History
DepositionJun 5, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bifunctional deaminase/diphosphatase
B: Bifunctional deaminase/diphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,48211
Polymers46,9242
Non-polymers5599
Water6,503361
1
A: Bifunctional deaminase/diphosphatase
hetero molecules

A: Bifunctional deaminase/diphosphatase
hetero molecules

A: Bifunctional deaminase/diphosphatase
hetero molecules

B: Bifunctional deaminase/diphosphatase
hetero molecules

B: Bifunctional deaminase/diphosphatase
hetero molecules

B: Bifunctional deaminase/diphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,44733
Polymers140,7716
Non-polymers1,67627
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_564-z+1/2,-x+1,y-1/21
crystal symmetry operation10_655-y+1,z+1/2,-x+1/21
crystal symmetry operation3_645-x+1,y-1/2,-z+1/21
crystal symmetry operation5_554z,x,y-11
crystal symmetry operation12_664-y+3/2,-z+1,x-1/21
Buried area23230 Å2
ΔGint-133.1 kcal/mol
Surface area41290 Å2
MethodPISA
2
A: Bifunctional deaminase/diphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6484
Polymers23,4621
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
B: Bifunctional deaminase/diphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8347
Polymers23,4621
Non-polymers3726
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)110.700, 110.700, 110.700
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-212-

HOH

21A-288-

HOH

31A-369-

HOH

41B-225-

HOH

51B-271-

HOH

61B-469-

HOH

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Components

#1: Protein Bifunctional deaminase/diphosphatase / MjDCD-DUT / DCD/DUT


Mass: 23461.854 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: MJ0430 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL
References: UniProt: Q57872, dCTP deaminase, dUTP diphosphatase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 2.41 Å3/Da / Density % sol: 48.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: nanopure water, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 7.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110-20 mg/mlprotein1drop
2150 mM1reservoirNaCl
32 mMdithiothreitol1reservoir
450 mMsodium HEPES1reservoirpH7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 16, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.42→45 Å / Num. obs: 84993 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 56.3
Reflection shellResolution: 1.42→1.47 Å / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 7.5 / Rsym value: 0.358 / % possible all: 100
Reflection
*PLUS
Num. measured all: 655273
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXmodel building
SHELXL-97refinement
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.42→45 Å / Num. parameters: 13127 / Num. restraintsaints: 11979 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2028 4251 5.3 %RANDOM
Rwork0.1853 ---
obs0.186 80707 99.8 %-
all-80707 --
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 2914 / Occupancy sum non hydrogen: 3278.81
Refinement stepCycle: LAST / Resolution: 1.42→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2886 0 36 361 3283
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0314
X-RAY DIFFRACTIONs_zero_chiral_vol0.06
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.067
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.029
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.067
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 45 Å / Rfactor Rfree: 0.22 / Rfactor Rwork: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.031
X-RAY DIFFRACTIONs_chiral_restr0.06

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