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- PDB-1w2y: The crystal structure of a complex of Campylobacter jejuni dUTPas... -

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Basic information

Entry
Database: PDB / ID: 1w2y
TitleThe crystal structure of a complex of Campylobacter jejuni dUTPase with substrate analogue dUpNHp
ComponentsDEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDE HYDROLASE
KeywordsHYDROLASE / DUTP PYROPHOSPHATASE / DIMERIC / LIGAND COMPLEX / MAGNESIUM IONS / PATHOGEN / DRUG TARGET
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-DIPHOSPHATE / dUTPase / :
Similarity search - Component
Biological speciesCAMPYLOBACTER JEJUNI (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsMoroz, O.V. / Harkiolaki, M. / Galperin, M.Y. / Vagin, A.A. / Gonzalez-Pacanowska, D. / Wilson, K.S.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: The Crystal Structure of a Complex of Campylobacter Jejuni Dutpase with Substrate Analogue Sheds Light on the Mechanism and Suggests the "Basic Module" for Dimeric D(C/U)Tpases
Authors: Moroz, O.V. / Harkiolaki, M. / Galperin, M.Y. / Vagin, A.A. / Gonzalez-Pacanowska, D. / Wilson, K.S.
History
DepositionJul 9, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2004Provider: 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 / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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.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.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)55,02410
Polymers54,1032
Non-polymers9208
Water6,900383
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)66.963, 70.629, 92.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDE HYDROLASE / PUTATIVE DUTPASE


Mass: 27051.742 Da / Num. of mol.: 2
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, dUTP diphosphatase
#2: Chemical ChemComp-DUN / 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-DIPHOSPHATE / 2,4(1H,3H)-PYRIMIDINEDIONE / 1-[2-DEOXY-5-O-[HYDROXY(PHOSPHONOAMINO)PHOSPHINYL]-BETA-D-ERYTHRO-PENTOFURANOSYL]-


Mass: 387.177 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N3O10P2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / 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 Å3/Da / Density % sol: 39 %
Crystal growpH: 7
Details: 25-30% MPD, 5% ISOPROPANOL, 50 MM MG-ACETATE, 100 MM HEPES PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.92
DetectorDate: Jul 14, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 53061 / % possible obs: 99.4 % / Observed criterion σ(I): 2.7 / Redundancy: 5.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 34
Reflection shellResolution: 1.65→1.71 Å / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.7 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OGK

1ogk


Resolution: 1.65→55.9 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.553 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS ENTRY CONTAINS ATOMS WHICH HAVE BEEN WITH AN OCCUPANCY OF 0.00.
RfactorNum. reflection% reflectionSelection details
Rfree0.194 2693 5.1 %RANDOM
Rwork0.151 ---
obs0.153 50185 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å20 Å2
2---0.23 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.65→55.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3599 0 54 383 4036
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223603
X-RAY DIFFRACTIONr_bond_other_d0.0010.023208
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.9524867
X-RAY DIFFRACTIONr_angle_other_deg1.22237436
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8725427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.64325.09167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2715636
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.1951512
X-RAY DIFFRACTIONr_chiral_restr0.1040.2534
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023931
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02739
X-RAY DIFFRACTIONr_nbd_refined0.2480.2964
X-RAY DIFFRACTIONr_nbd_other0.1780.23411
X-RAY DIFFRACTIONr_nbtor_refined0.1940.21832
X-RAY DIFFRACTIONr_nbtor_other0.0890.21905
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2271
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2540.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.13422802
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.59933401
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.32761790
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.414101466
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: 1.65→1.7 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.224 183
Rwork0.173 3564
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5714-0.3358-1.0711.44191.09926.3603-0.1842-0.0061-0.21730.10050.1585-0.22050.52390.48280.0256-0.14750.06310.0163-0.112-0.0284-0.067263.88345.61712.724
21.8003-0.2759-0.29992.55981.2343.56540.0667-0.10080.193-0.14090.2906-0.8328-0.17840.5297-0.3573-0.1869-0.02750.0393-0.0336-0.10660.095169.59961.2611.8
31.4153-0.7678-0.33151.6570.65441.22890.0460.1215-0.1076-0.161-0.0038-0.0335-0.0149-0.0184-0.0422-0.181-0.00590.017-0.1406-0.0215-0.155752.45556.1016.559
43.9279-1.4434-2.9642.55321.82234.59210.32060.26680.3509-0.3579-0.24820.1626-0.5319-0.4423-0.07240.03320.1423-0.0193-0.09920.0018-0.071830.48986.1411.547
53.69070.1149-1.62072.0325-0.32864.89880.1791-0.20140.7661-0.0708-0.0085-0.2768-0.92750.3432-0.17060.1057-0.05180.0369-0.1423-0.03480.066546.56187.85215.832
61.8441-1.2301-0.22372.37120.44491.34730.029-0.0024-0.0147-0.0266-0.05320.1834-0.118-0.18070.0243-0.17610.010.0157-0.1609-0.0137-0.173638.12971.51816.098
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 25
2X-RAY DIFFRACTION2A165 - 250
3X-RAY DIFFRACTION3A26 - 164
4X-RAY DIFFRACTION4B1 - 25
5X-RAY DIFFRACTION5B165 - 250
6X-RAY DIFFRACTION6B25 - 88
7X-RAY DIFFRACTION6B97 - 116
8X-RAY DIFFRACTION6B124 - 164

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