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- PDB-2c56: A comparative study of uracil DNA glycosylases from human and her... -

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Basic information

Entry
Database: PDB / ID: 2c56
TitleA comparative study of uracil DNA glycosylases from human and herpes simplex virus type 1
ComponentsURACIL DNA GLYCOSYLASE
KeywordsHYDROLASE / URACIL DNA GLYCOSYLASE / DNA REPAIR / DNA DAMAGE / GLYCOSIDASE
Function / homology
Function and homology information


base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / uracil DNA N-glycosylase activity / host cell nucleus
Similarity search - Function
Uracil-DNA glycosylase family 1 / Uracil DNA glycosylase superfamily / UreE urease accessory protein, C-terminal domain / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily ...Uracil-DNA glycosylase family 1 / Uracil DNA glycosylase superfamily / UreE urease accessory protein, C-terminal domain / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
sucrose / Uracil-DNA glycosylase
Similarity search - Component
Biological speciesHUMAN HERPESVIRUS 1 (Herpes simplex virus type 1)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKrusong, K. / Carpenter, E.P. / Bellamy, S.R.W. / Savva, R. / Baldwin, G.S.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: A Comparative Study of Uracil-DNA Glycosylases from Human and Herpes Simplex Virus Type 1.
Authors: Krusong, K. / Carpenter, E.P. / Bellamy, S.R.W. / Savva, R. / Baldwin, G.S.
History
DepositionOct 26, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Derived calculations / Other ...Derived calculations / Other / Structure summary / Version format compliance
Revision 1.2May 22, 2019Group: Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_database_status.status_code_sf
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: URACIL DNA GLYCOSYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6842
Polymers27,3411
Non-polymers3421
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)42.040, 61.117, 43.392
Angle α, β, γ (deg.)90.00, 92.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein URACIL DNA GLYCOSYLASE


Mass: 27341.418 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN HERPESVIRUS 1 (Herpes simplex virus type 1)
Plasmid: D88N/H20N / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P10186, uridine nucleosidase
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCUTS URACIL RESIDUES FROM THE DNA. ENGINEERED RESIDUE IN CHAIN A, ASP 178 TO ASN ENGINEERED RESIDUE ...CUTS URACIL RESIDUES FROM THE DNA. ENGINEERED RESIDUE IN CHAIN A, ASP 178 TO ASN ENGINEERED RESIDUE IN CHAIN A, HIS 300 TO ASN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 34.51 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 12927 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 3.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.56
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 5.26 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UDG

1udg


Resolution: 2.1→29.59 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1105069.29 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESIDUES 1 - 16 IN THIS MOLECULE DO NOT APPEAR IN THE ELECTRON DENSITY AND ARE PRESUMED TO BE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.212 646 5 %RANDOM
Rwork0.151 ---
obs0.151 12912 99.8 %-
Solvent computationSolvent model: CNS BULK SOLVENT MODEL USED / Bsol: 52.0358 Å2 / ksol: 0.335261 e/Å3
Displacement parametersBiso mean: 14.71 Å2
Baniso -1Baniso -2Baniso -3
1-2.46 Å20 Å2-3.85 Å2
2---2.57 Å20 Å2
3---0.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.07 Å0.02 Å
Refinement stepCycle: LAST / Resolution: 2.1→29.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1797 0 23 259 2079
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.13
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_mcangle_it1.752
X-RAY DIFFRACTIONc_scbond_it3.342
X-RAY DIFFRACTIONc_scangle_it4.022.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.205 106 5 %
Rwork0.14 2024 -
obs--100 %

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