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- PDB-2hrm: Crystal structure of dUTPase complexed with substrate analogue me... -

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Basic information

Entry
Database: PDB / ID: 2hrm
TitleCrystal structure of dUTPase complexed with substrate analogue methylene-dUTP
ComponentsDeoxyuridine 5'-triphosphate nucleotidohydrolase
KeywordsHYDROLASE / JELLY ROLL / ENZYME-SUBSTRATE ANALOGUE LIGAND COMPLEX
Function / homology
Function and homology information


dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / protein homotrimerization / magnesium ion binding / protein-containing complex / identical protein binding / cytosol
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
Chem-UC5 / Deoxyuridine 5'-triphosphate nucleotidohydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBarabas, O. / Kovari, J. / Tapai, R. / Vertessy, B.G.
Citation
Journal: Proteins / Year: 2008
Title: Methylene substitution at the alpha-beta bridging position within the phosphate chain of dUDP profoundly perturbs ligand accommodation into the dUTPase active site.
Authors: Kovari, J. / Barabas, O. / Varga, B. / Bekesi, A. / Tolgyesi, F. / Fidy, J. / Nagy, J. / Vertessy, B.G.
#1: Journal: J.Biol.Chem. / Year: 2004
Title: Structural Insights into the Catalytic Mechanism of Phosphate Ester Hydrolysis by dUTPase.
Authors: Barabas, O. / Pongracz, V. / Kovari, J. / Wilmanns, M. / Vertessy, B.G.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Atomic Resolution Structure of Escherichia Coli Dutpase Determined Ab Initio
Authors: Gonzalez, A. / Larsson, G. / Persson, R. / Cedergren-Zeppezauer, E.
History
DepositionJul 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Aug 30, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / 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 / _diffrn_source.pdbx_synchrotron_site / _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)16,7513
Polymers16,3031
Non-polymers4482
Water2,450136
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)50,2539
Polymers48,9083
Non-polymers1,3456
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area12570 Å2
ΔGint-52 kcal/mol
Surface area15660 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)75.650, 75.650, 101.558
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-864-

HOH

21A-875-

HOH

DetailsThe biological assembly is a trimer generated from the monomer in the asymmetric unit by the operations: 1-y,1+x-y,z and -x+y,1-x,z

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Components

#1: Protein Deoxyuridine 5'-triphosphate nucleotidohydrolase / dUTPase / dUTP pyrophosphatase


Mass: 16302.615 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dut / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P06968, dUTP diphosphatase
#2: Chemical ChemComp-UC5 / 2'-DEOXY-5'-O-[(S)-HYDROXY(PHOSPHONOMETHYL)PHOSPHORYL]URIDINE


Mass: 386.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O10P2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.57 Å3/Da / Density % sol: 52.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 20% PEG 3350, 0.2M SODIUM ACETATE, 0.1M TRIS, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.85 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Details: mirror
RadiationMonochromator: Si [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.85 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 19276 / Num. obs: 19276 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.16 % / Biso Wilson estimate: 28.27 Å2 / Rsym value: 0.048 / Net I/σ(I): 14.5
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 3.19 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 3034 / Rsym value: 0.457 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EUW

1euw


Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.962 / SU B: 4.355 / SU ML: 0.063 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19559 987 5.1 %RANDOM
Rwork0.16823 ---
all0.16956 18283 --
obs0.16956 18283 99.13 %-
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: 21.045 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1012 0 28 136 1176
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221099
X-RAY DIFFRACTIONr_bond_other_d0.0010.021050
X-RAY DIFFRACTIONr_angle_refined_deg1.6772.0111509
X-RAY DIFFRACTIONr_angle_other_deg0.86132439
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4825147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.74625.12839
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.25915178
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.198154
X-RAY DIFFRACTIONr_chiral_restr0.1120.2181
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021207
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02196
X-RAY DIFFRACTIONr_nbd_refined0.190.2125
X-RAY DIFFRACTIONr_nbd_other0.1820.2880
X-RAY DIFFRACTIONr_nbtor_refined0.1580.2478
X-RAY DIFFRACTIONr_nbtor_other0.0810.2591
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.269
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1350.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2130.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.213
X-RAY DIFFRACTIONr_mcbond_it1.7021.5736
X-RAY DIFFRACTIONr_mcbond_other0.1161.5286
X-RAY DIFFRACTIONr_mcangle_it2.92661137
X-RAY DIFFRACTIONr_scbond_it5.3310425
X-RAY DIFFRACTIONr_scangle_it6.90320366
LS refinement shellResolution: 1.703→1.747 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 68 -
Rwork0.264 1325 -
obs-1393 99.57 %
Refinement TLS params.Method: refined / Origin x: 27.5011 Å / Origin y: 15.8307 Å / Origin z: 4.9283 Å
111213212223313233
T-0.0331 Å20.0056 Å2-0.0027 Å2--0.0276 Å2-0.0299 Å2---0.0179 Å2
L0.69 °20.3476 °20.0289 °2-0.8166 °20.0508 °2--0.3262 °2
S-0.0312 Å °0.0368 Å °-0.0444 Å °-0.0241 Å °-0.0454 Å °0.0599 Å °0.0226 Å °-0.0542 Å °0.0766 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1371 - 137
2X-RAY DIFFRACTION1AB7771

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