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- PDB-1ssp: WILD-TYPE URACIL-DNA GLYCOSYLASE BOUND TO URACIL-CONTAINING DNA -

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Basic information

Entry
Database: PDB / ID: 1ssp
TitleWILD-TYPE URACIL-DNA GLYCOSYLASE BOUND TO URACIL-CONTAINING DNA
Components
  • 5'-D(*AP*AP*AP*GP*AP*TP*AP*AP*CP*AP*G)-3'
  • 5'-D(*CP*TP*GP*TP*(D1P)P*AP*TP*CP*TP*T)-3'
  • URACIL-DNA GLYCOSYLASE
KeywordsHYDROLASE/DNA / DNA GLYCOSYLASE / DNA BASE EXCISION REPAIR / URACIL / DNA / PROTEIN/DNA / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / depyrimidination / Displacement of DNA glycosylase by APEX1 / single strand break repair / isotype switching / uracil DNA N-glycosylase activity / ribosomal small subunit binding / somatic hypermutation of immunoglobulin genes / Recognition and association of DNA glycosylase with site containing an affected pyrimidine ...base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / depyrimidination / Displacement of DNA glycosylase by APEX1 / single strand break repair / isotype switching / uracil DNA N-glycosylase activity / ribosomal small subunit binding / somatic hypermutation of immunoglobulin genes / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Chromatin modifications during the maternal to zygotic transition (MZT) / base-excision repair / damaged DNA binding / negative regulation of apoptotic process / mitochondrion / nucleoplasm / 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
URACIL / DNA / DNA (> 10) / Uracil-DNA glycosylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsParikh, S.S. / Mol, C.D. / Slupphaug, G. / Bharati, S. / Krokan, H.E. / Tainer, J.A.
Citation
Journal: EMBO J. / Year: 1998
Title: Base excision repair initiation revealed by crystal structures and binding kinetics of human uracil-DNA glycosylase with DNA.
Authors: Parikh, S.S. / Mol, C.D. / Slupphaug, G. / Bharati, S. / Krokan, H.E. / Tainer, J.A.
#1: Journal: Nature / Year: 1996
Title: A Nucleotide-Flipping Mechanism from the Structure of Human Uracil-DNA Glycosylase Bound to DNA
Authors: Slupphaug, G. / Mol, C.D. / Kavli, B. / Arvai, A.S. / Krokan, H.E. / Tainer, J.A.
History
DepositionApr 28, 1999Deposition site: BNL / Processing site: NDB
Revision 1.0May 6, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: 5'-D(*CP*TP*GP*TP*(D1P)P*AP*TP*CP*TP*T)-3'
B: 5'-D(*AP*AP*AP*GP*AP*TP*AP*AP*CP*AP*G)-3'
E: URACIL-DNA GLYCOSYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9484
Polymers31,8363
Non-polymers1121
Water4,774265
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.700, 48.500, 65.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212

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Components

#1: DNA chain 5'-D(*CP*TP*GP*TP*(D1P)P*AP*TP*CP*TP*T)-3'


Mass: 2892.878 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*AP*AP*AP*GP*AP*TP*AP*AP*CP*AP*G)-3'


Mass: 3399.276 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: COMPLEXED WITH URACIL
#3: Protein URACIL-DNA GLYCOSYLASE / EC 3.2.2.3 / UDG / UNG


Mass: 25544.137 Da / Num. of mol.: 1 / Fragment: MITOCHONDRIAL
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P13051, uridine nucleosidase
#4: Chemical ChemComp-URA / URACIL


Mass: 112.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4N2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 3 Å3/Da / Density % sol: 59 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 4000, 100 MM HEPES PH 6.5, 10% DIOXANE, 1 MM DITHIOTHREITOL, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2HEPES11
3DIOXANE11
4DITHIOTHREITOL11
5H2O11
6PEG 400012
7HEPES12
Crystal
*PLUS
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 %PEG40001reservoir
2100 mM1reservoirpH6.5
310 %dioxane1reservoir
41 mMdithiothreitol1reservoir
51
61
71

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorDate: Apr 19, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 30394 / % possible obs: 97.5 % / Redundancy: 3.3 % / Rsym value: 0.06 / Net I/σ(I): 18.9
Reflection shellResolution: 1.9→1.97 Å / Mean I/σ(I) obs: 4.2 / Rsym value: 0.212 / % possible all: 87.1
Reflection
*PLUS
Num. measured all: 105498 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 87.1 % / Rmerge(I) obs: 0.212

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AKZ

1akz


Resolution: 1.9→20 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.245 -10 %RANDOM
Rwork0.198 ---
obs0.198 29732 97.58 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--11.6 Å20 Å20 Å2
2--5.74 Å20 Å2
3---5.95 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1808 417 8 265 2498
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.34
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.9→1.99 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.292 --
Rwork0.268 2953 -
obs--85.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM_NDBX.DNATOP_NDBX.DNA
X-RAY DIFFRACTION3PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / Num. reflection obs: 30363 / σ(F): 2 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.292 / Rfactor Rwork: 0.268

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