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- PDB-2ugi: PROTEIN MIMICRY OF DNA FROM CRYSTAL STRUCTURES OF THE URACIL GLYC... -

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Basic information

Entry
Database: PDB / ID: 2ugi
TitlePROTEIN MIMICRY OF DNA FROM CRYSTAL STRUCTURES OF THE URACIL GLYCOSYLASE INHIBITOR PROTEIN AND ITS COMPLEX WITH ESCHERICHIA COLI URACIL-DNA GLYCOSYLASE
ComponentsURACIL-DNA GLYCOSYLASE INHIBITOR
KeywordsHYDROLASE INHIBITOR / PROTEIN MIMICRY OF DNA / PROTEIN INHIBITOR
Function / homologyBacteriophage PBS2, uracil-glycosylase inhibitor / Bacteriophage PBS2, uracil-glycosylase inhibitor / Uracil-DNA glycosylase inhibitor / Uracil-DNA glycosylase inhibitor / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / IMIDAZOLE / Uracil-DNA glycosylase inhibitor
Function and homology information
Biological speciesBacillus phage PBS2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPutnam, C.D. / Arvai, A.S. / Mol, C.D. / Tainer, J.A.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Protein mimicry of DNA from crystal structures of the uracil-DNA glycosylase inhibitor protein and its complex with Escherichia coli uracil-DNA glycosylase
Authors: Putnam, C.D. / Shroyer, M.J. / Lundquist, A.J. / Mol, C.D. / Arvai, A.S. / Mosbaugh, D.W. / Tainer, J.A.
History
DepositionNov 6, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 25, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: URACIL-DNA GLYCOSYLASE INHIBITOR
B: URACIL-DNA GLYCOSYLASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0343
Polymers18,9652
Non-polymers691
Water1,27971
1
A: URACIL-DNA GLYCOSYLASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5522
Polymers9,4831
Non-polymers691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: URACIL-DNA GLYCOSYLASE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)9,4831
Polymers9,4831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.092, 59.387, 73.583
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.35163, 0.01929, 0.93594), (-0.00942, -0.99981, 0.01707), (0.93609, -0.00282, 0.35175)
Vector: 14.17055, 37.25146, -9.82261)

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Components

#1: Protein URACIL-DNA GLYCOSYLASE INHIBITOR / UGI


Mass: 9482.674 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage PBS2 (virus) / Cellular location: CYTOPLASM / Plasmid: PZWTAC1 / Cellular location (production host): CYTOPLASM / Gene (production host): TAC / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: P14739
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.4 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 293 K / pH: 8.2
Details: (NH4)2SO4, IMIDAZOLE, MALATE, (NH4)2SO4, pH 8.2, temperature 293.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1(NH4)2SO411
2IMIDAZOLE11
3MALATE11
4(NH4)2SO412
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
184 %satammonium sulfate1reservoir
2200 mMimidazole/malate1reservoir
31
41

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.918
DetectorType: PRINCETON 2K / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 9507 / % possible obs: 95.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 35.2 Å2 / Rsym value: 0.069 / Net I/σ(I): 19.7
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 3 % / Mean I/σ(I) obs: 6.2 / Rsym value: 0.251 / % possible all: 91.8
Reflection
*PLUS
Num. obs: 9493 / % possible obs: 95.3 % / Num. measured all: 34065 / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
% possible obs: 91.9 % / Num. unique obs: 883 / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 8.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: UGI FROM THE HUMAN UDG:UGI CRYSTAL STRUCTURE

Resolution: 2.2→20 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.28 958 10 %RANDOM
Rwork0.227 ---
all-9435 --
obs-9435 96.1 %-
Displacement parametersBiso mean: 47 Å2
Baniso -1Baniso -2Baniso -3
1--8.34 Å20 Å20 Å2
2--5.643 Å20 Å2
3---2.7 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1308 0 5 71 1384
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_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.25
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.556
X-RAY DIFFRACTIONx_mcangle_it2.724
X-RAY DIFFRACTIONx_scbond_it2.417
X-RAY DIFFRACTIONx_scangle_it3.888
LS refinement shellResolution: 2.2→2.3 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.363 95 8 %
Rwork0.362 1081 -
obs--97.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARHCSDX.PROTOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.227
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.25
LS refinement shell
*PLUS
Rfactor obs: 0.362

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