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- PDB-3mbq: Crystal structure of deoxyuridine 5-triphosphate nucleotidohydrol... -

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Basic information

Entry
Database: PDB / ID: 3mbq
TitleCrystal structure of deoxyuridine 5-triphosphate nucleotidohydrolase from Brucella melitensis, orthorhombic crystal form
ComponentsDeoxyuridine 5'-triphosphate nucleotidohydrolase
KeywordsHYDROLASE / ALS COLLABORATIVE CRYSTALLOGRAPHY / DEOXYURIDINE 5-TRIPHOSPHATE NUCLEOTIDOHYDROLASE / Metal-binding / Nucleotide metabolism / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / magnesium ion binding
Similarity search - Function
Deoxyuridine triphosphate nucleotidohydrolase / 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
Deoxyuridine 5'-triphosphate nucleotidohydrolase
Similarity search - Component
Biological speciesBrucella melitensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of deoxyuridine 5-triphosphate nucleotidohydrolase from Brucella melitensis, orthorhombic crystal form
Authors: Abendroth, J. / Sankaran, T. / Gardberg, A. / Staker, B.
History
DepositionMar 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Sep 6, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Deoxyuridine 5'-triphosphate nucleotidohydrolase
B: Deoxyuridine 5'-triphosphate nucleotidohydrolase
C: Deoxyuridine 5'-triphosphate nucleotidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,10118
Polymers56,9063
Non-polymers1,19515
Water6,215345
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13030 Å2
ΔGint-93 kcal/mol
Surface area16010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.560, 95.890, 100.350
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 nucleotidohydrolase / dUTPase / dUTP pyrophosphatase


Mass: 18968.600 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis (bacteria) / Strain: 2308 / Gene: dut, BAB1_1687 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2YRG4, dUTP diphosphatase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 2.14 Å3/Da / Density % sol: 42.45 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: HR CRYSTAL HT SCREEN, E5: 2M AMMONIUM SUPHATE, 5% ISO-PROPANOL, BRABA.10050.A AT 9.7MG/ML, pH 8.50, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 29277 / Num. obs: 29269 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.9 % / Biso Wilson estimate: 25.79 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 19.54
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 9 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 4.7 / Num. unique all: 2101 / % possible all: 100

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1dup modified with ccp4 program chainsaw

1dup


Resolution: 2.1→47.94 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / SU B: 7.559 / SU ML: 0.093 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.181 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1476 5.1 %RANDOM
Rwork0.166 ---
all0.169 29277 --
obs0.169 29092 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2--0.22 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.1→47.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3068 0 70 345 3483
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223206
X-RAY DIFFRACTIONr_bond_other_d0.0010.022238
X-RAY DIFFRACTIONr_angle_refined_deg1.4642.0154345
X-RAY DIFFRACTIONr_angle_other_deg0.86635444
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.345416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.70622.985134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.8215535
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4251536
X-RAY DIFFRACTIONr_chiral_restr0.0930.2503
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213534
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02618
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8231.52032
X-RAY DIFFRACTIONr_mcbond_other0.2181.5831
X-RAY DIFFRACTIONr_mcangle_it1.52523273
X-RAY DIFFRACTIONr_scbond_it2.6431174
X-RAY DIFFRACTIONr_scangle_it4.3274.51065
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 115 -
Rwork0.177 1974 -
obs--99.71 %
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)
10.56390.0717-0.28110.3857-0.62351.21460.0653-0.0556-0.06290.10260.00470.0534-0.0962-0.0416-0.070.08570.00240.01260.14440.02570.02713.6596.29925.001
20.56140.0915-0.04290.664-0.29640.47930.0534-0.00360.07540.0816-0.00250.0469-0.11910.022-0.05090.0736-0.00150.02310.11950.00010.018420.20820.44910.932
30.9852-0.085-0.27410.7675-0.18520.57280.0350.0014-0.1037-0.0389-0.0251-0.07290.00730.1751-0.00990.03050.006-0.00690.16180.00260.035629.5631.35812.759
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 142
2X-RAY DIFFRACTION1A200 - 205
3X-RAY DIFFRACTION1A158 - 345
4X-RAY DIFFRACTION2B8 - 139
5X-RAY DIFFRACTION2B200 - 205
6X-RAY DIFFRACTION2B158 - 334
7X-RAY DIFFRACTION3C8 - 151
8X-RAY DIFFRACTION3C201 - 206
9X-RAY DIFFRACTION3C158 - 344

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