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- PDB-1ugi: URACIL-DNA GLYCOSYLASE INHIBITOR PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1ugi
TitleURACIL-DNA GLYCOSYLASE INHIBITOR PROTEIN
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: 1.55 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 4, 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

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Assembly

Deposited unit
A: URACIL-DNA GLYCOSYLASE INHIBITOR
B: URACIL-DNA GLYCOSYLASE INHIBITOR
C: URACIL-DNA GLYCOSYLASE INHIBITOR
D: URACIL-DNA GLYCOSYLASE INHIBITOR
E: URACIL-DNA GLYCOSYLASE INHIBITOR
F: URACIL-DNA GLYCOSYLASE INHIBITOR
G: URACIL-DNA GLYCOSYLASE INHIBITOR
H: URACIL-DNA GLYCOSYLASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,68132
Polymers75,8618
Non-polymers1,82024
Water10,106561
1
A: URACIL-DNA GLYCOSYLASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5792
Polymers9,4831
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: URACIL-DNA GLYCOSYLASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6213
Polymers9,4831
Non-polymers1382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: URACIL-DNA GLYCOSYLASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8556
Polymers9,4831
Non-polymers3725
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: URACIL-DNA GLYCOSYLASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7865
Polymers9,4831
Non-polymers3034
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: URACIL-DNA GLYCOSYLASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9517
Polymers9,4831
Non-polymers4686
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: URACIL-DNA GLYCOSYLASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6213
Polymers9,4831
Non-polymers1382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: URACIL-DNA GLYCOSYLASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6483
Polymers9,4831
Non-polymers1652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: URACIL-DNA GLYCOSYLASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6213
Polymers9,4831
Non-polymers1382
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.800, 59.400, 79.800
Angle α, β, γ (deg.)73.67, 85.55, 66.46
Int Tables number1
Cell settingtriclinic
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99737, -0.05262, 0.04989), (0.03955, -0.97143, -0.23402), (0.06078, -0.23143, 0.97095)-0.81482, -0.41685, -3.70572
2given(0.63329, 0.77389, 0.00676), (0.77328, -0.6331, 0.03503), (0.03138, -0.01696, -0.99936)37.43958, 25.45655, 13.69368
3given(-0.67192, -0.73709, -0.07222), (-0.73019, 0.643, 0.23104), (-0.12386, 0.20798, -0.97026)35.80038, 25.01386, 17.28484
4given(0.6759, 0.7312, -0.09227), (-0.73325, 0.67978, 0.01573), (0.07423, 0.05702, 0.99561)20.89913, 36.7387, 37.46319
5given(-0.66131, -0.73257, -0.16129), (0.7484, -0.62986, -0.20777), (0.05062, -0.25811, 0.96479)19.75451, 37.03503, 33.25365
6given(0.99405, 0.05443, 0.09433), (0.05663, -0.99818, -0.02088), (0.09302, 0.0261, -0.99532)31.35763, 61.9147, 50.99107
7given(-0.99026, -0.00736, 0.139), (0.02258, 0.97689, 0.21255), (-0.13736, 0.21362, -0.96721)30.3963, 62.24492, 54.83612

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Components

#1: Protein
URACIL-DNA GLYCOSYLASE INHIBITOR / UGI


Mass: 9482.674 Da / Num. of mol.: 8
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 561 / 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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 277 K / pH: 8.2 / Details: pH 8.2, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1(NH4)2SO411
2IMIDAZOLE11
3MALATE11
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
184 %satammonium sulfate1reservoir
2200 mMimidazole/malate1reservoir
31

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.918
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. obs: 95452 / % possible obs: 86.7 % / Redundancy: 2.3 % / Rsym value: 0.064 / Net I/σ(I): 16.9
Reflection shellResolution: 1.55→1.59 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2 / Rsym value: 0.368 / % possible all: 86.5
Reflection
*PLUS
Num. measured all: 221922 / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
% possible obs: 86.5 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ORTHORHOMBIC CRYSTAL FORM OF FREE UGI

Resolution: 1.55→20 Å / Num. parameters: 24407 / Num. restraintsaints: 22880 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2886 9346 10 %RANDOM
obs0.2218 86111 86.5 %-
all-86111 --
Solvent computationSolvent model: BABINET'S PRINCIPLE SCALING
Refine analyzeNum. disordered residues: 24
Refinement stepCycle: LAST / Resolution: 1.55→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5414 0 120 561 6095
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d1.97
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.222 / Rfactor Rfree: 0.289
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 1.55 Å / Lowest resolution: 1.62 Å / Rfactor Rfree: 0.348 / Num. reflection obs: 9225 / Rfactor obs: 0.329

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