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- PDB-2cic: THE CRYSTAL STRUCTURE OF A COMPLEX OF CAMPYLOBACTER JEJUNI DUTPAS... -

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Basic information

Entry
Database: PDB / ID: 2cic
TitleTHE CRYSTAL STRUCTURE OF A COMPLEX OF CAMPYLOBACTER JEJUNI DUTPASE WITH SUBSTRATE ANALOGUE DUPNHPP
ComponentsDEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDE HYDROLASE
KeywordsHYDROLASE / LIGAND COMPLEX / DRUG TARGET / DUTP PYROPHOSPHATASE
Function / homology
Function and homology information


dUTP diphosphatase / dUTP diphosphatase activity / metal ion binding
Similarity search - Function
all-alpha NTP pyrophosphatase fold / Type II deoxyuridine triphosphatase / dUTPase/dCTP pyrophosphatase / dUTPase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE / dUTPase / :
Similarity search - Component
Biological speciesCAMPYLOBACTER JEJUNI (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMoroz, O.V. / Harkiolaki, M. / Gonzalez-Pacanowska, D. / Wilson, K.S.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: The Crystal Structure of the Leishmania Major Deoxyuridine Triphosphate Nucleotidohydrolase in Complex with Nucleotide Analogues, Dump, and Deoxyuridine.
Authors: Hemsworth, G.R. / Moroz, O.V. / Fogg, M.J. / Scott, B. / Bosch-Navarrete, C. / Gonzalez-Pacanowska, D. / Wilson, K.S.
History
DepositionMar 17, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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

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Assembly

Deposited unit
A: DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5684
Polymers27,0521
Non-polymers5163
Water8,611478
1
A: DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDE HYDROLASE
hetero molecules

A: DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1358
Polymers54,1032
Non-polymers1,0326
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area6090 Å2
ΔGint-66.4 kcal/mol
Surface area19160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.397, 93.397, 143.634
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-2144-

HOH

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Components

#1: Protein DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDE HYDROLASE


Mass: 27051.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAMPYLOBACTER JEJUNI (Campylobacter) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9PMK9, UniProt: Q0P8G4*PLUS
#2: Chemical ChemComp-DUP / 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 478 / 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: 2.9 Å3/Da / Density % sol: 57 %
Crystal growDetails: 3.5 M SODIUM FORMATE PH 7.0, 20 MM MAGNESIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.979
DetectorDate: Jul 21, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 33092 / % possible obs: 97.8 % / Observed criterion σ(I): 3 / Redundancy: 8.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 37.1
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.3 / % possible all: 90.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W2Y

1w2y


Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.698 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1700 5.1 %RANDOM
Rwork0.159 ---
obs0.162 31466 94.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20 Å20 Å2
2--0.54 Å20 Å2
3----1.08 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1851 0 30 478 2359
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221906
X-RAY DIFFRACTIONr_bond_other_d0.0020.021672
X-RAY DIFFRACTIONr_angle_refined_deg1.9281.9612581
X-RAY DIFFRACTIONr_angle_other_deg1.96733911
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5445221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.78425.93896
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.98415349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.907154
X-RAY DIFFRACTIONr_chiral_restr0.1990.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022067
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02373
X-RAY DIFFRACTIONr_nbd_refined0.3490.2874
X-RAY DIFFRACTIONr_nbd_other0.260.22116
X-RAY DIFFRACTIONr_nbtor_refined0.1960.2963
X-RAY DIFFRACTIONr_nbtor_other0.0950.21053
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3310.2468
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2810.239
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2850.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3920.269
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4831.51442
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.84221780
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.743971
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7864.5801
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: 1.7→1.75 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.272 101
Rwork0.19 1366

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