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

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Basic information

Entry
Database: PDB / ID: 3lqw
TitleCrystal structure of deoxyuridine 5-triphosphate nucleotidohydrolase from Entamoeba histolytica
ComponentsDeoxyuridine 5'-triphosphate nucleotidohydrolase
KeywordsHYDROLASE / EMERALD BIOSTRUCTURES / ALS COLLABORATIVE CRYSTALLOGRAPHY / DEOXYURIDINA 5-TRIPHOSPHATE NUCLEOTIDOHYDROLASE / 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 speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of deoxyuridine 5-triphosphate nucleotidohydrolase from Entamoeba histolytica
Authors: Abendroth, J. / Sankaran, B. / Arakaki, T. / Staker, B.
History
DepositionFeb 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1643
Polymers18,0091
Non-polymers1542
Water2,540141
1
A: Deoxyuridine 5'-triphosphate nucleotidohydrolase
hetero molecules

A: Deoxyuridine 5'-triphosphate nucleotidohydrolase
hetero molecules

A: Deoxyuridine 5'-triphosphate nucleotidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4919
Polymers54,0283
Non-polymers4626
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area10550 Å2
ΔGint-42 kcal/mol
Surface area15630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.140, 63.140, 108.370
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-150-

GOL

21A-150-

GOL

31A-143-

HOH

41A-144-

HOH

51A-155-

HOH

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Components

#1: Protein Deoxyuridine 5'-triphosphate nucleotidohydrolase


Mass: 18009.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Strain: HM-1:IMSS / Gene: EHI_189420 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C4M4M6
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.31 Å3/Da / Density % sol: 46.72 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8
Details: MD PACT SCREEN CONDITION D9: 100MM TRIS, 20% PEG 6000, 200MM LICL, ENHIA.01206.A AT 3.8 MG/ML, pH 8.0, 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 315r / Detector: CCD / Date: Jan 24, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. all: 39679 / Num. obs: 39194 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 18.91 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.65
Reflection shellResolution: 1.3→1.33 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.7 / % possible all: 91.5

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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 2hva modified with CCP4 program CHAINSAW

2hva


Resolution: 1.3→48.82 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.031 / SU ML: 0.02 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.038 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.155 1970 5 %RANDOM
Rwork0.132 ---
obs0.133 39193 98.8 %-
all-39679 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20.11 Å20 Å2
2--0.21 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.3→48.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1086 0 10 141 1237
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221125
X-RAY DIFFRACTIONr_bond_other_d0.0020.02763
X-RAY DIFFRACTIONr_angle_refined_deg1.7721.9711545
X-RAY DIFFRACTIONr_angle_other_deg0.96431883
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.755159
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.80623.67349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.55815198
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.345159
X-RAY DIFFRACTIONr_chiral_restr0.110.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021285
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02228
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_it1.8291.5702
X-RAY DIFFRACTIONr_mcbond_other0.5971.5288
X-RAY DIFFRACTIONr_mcangle_it2.90221154
X-RAY DIFFRACTIONr_scbond_it3.9053423
X-RAY DIFFRACTIONr_scangle_it5.7474.5378
X-RAY DIFFRACTIONr_rigid_bond_restr0.90311888
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.33 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.198 125 -
Rwork0.161 2563 -
obs--91.65 %

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