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- PDB-4l5n: Crystallographic Structure of HHV-1 Uracil-DNA Glycosylase comple... -

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Basic information

Entry
Database: PDB / ID: 4l5n
TitleCrystallographic Structure of HHV-1 Uracil-DNA Glycosylase complexed with the Bacillus phage PZA inhibitor protein p56
Components
  • Early protein GP1B
  • Uracil-DNA glycosylase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / UDG Inhibition / HYDROLASE-HYDROLASE INHIBITOR complex
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
Double Stranded RNA Binding Domain - #30 / : / : / Phage phi29, UDG inhibitor P56 / Double Stranded RNA Binding Domain / 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. ...Double Stranded RNA Binding Domain - #30 / : / : / Phage phi29, UDG inhibitor P56 / Double Stranded RNA Binding Domain / 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 / Other non-globular / Special / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Protein p56 / Uracil-DNA glycosylase
Similarity search - Component
Biological speciesHerpes simplex virus type 1 (Herpes simplex virus type 1)
Bacillus phage PZA (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsCole, A.R. / Sapir, O. / Ryzhenkova, K. / Baltulionis, G. / Hornyak, P. / Savva, R.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Architecturally diverse proteins converge on an analogous mechanism to inactivate Uracil-DNA glycosylase.
Authors: Cole, A.R. / Ofer, S. / Ryzhenkova, K. / Baltulionis, G. / Hornyak, P. / Savva, R.
History
DepositionJun 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2013Group: Database references
Revision 1.2Oct 23, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: Uracil-DNA glycosylase
B: Uracil-DNA glycosylase
C: Early protein GP1B
D: Early protein GP1B
E: Early protein GP1B
F: Early protein GP1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,66621
Polymers79,7806
Non-polymers88615
Water7,368409
1
A: Uracil-DNA glycosylase
C: Early protein GP1B
D: Early protein GP1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,42212
Polymers39,8903
Non-polymers5319
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-17 kcal/mol
Surface area15470 Å2
MethodPISA
2
A: Uracil-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3938
Polymers26,9801
Non-polymers4137
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Uracil-DNA glycosylase
E: Early protein GP1B
F: Early protein GP1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2459
Polymers39,8903
Non-polymers3546
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-12 kcal/mol
Surface area14580 Å2
MethodPISA
4
B: Uracil-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0983
Polymers26,9801
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
C: Early protein GP1B
D: Early protein GP1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0284
Polymers12,9102
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-2 kcal/mol
Surface area5950 Å2
MethodPISA
6
E: Early protein GP1B
F: Early protein GP1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1466
Polymers12,9102
Non-polymers2364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-2 kcal/mol
Surface area5760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.704, 91.375, 162.862
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsSubunits A and B are Monomers with Dimeric Inhibitors attached / Two Dimers consisting of C-D E-F

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Components

#1: Protein Uracil-DNA glycosylase / UDG / UNG


Mass: 26979.980 Da / Num. of mol.: 2 / Fragment: UNP residues 96-334
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Herpes simplex virus type 1 (Herpes simplex virus type 1)
Strain: strain 17 / Gene: UL2 / Production host: Escherichia coli (E. coli) / References: UniProt: P10186, uracil-DNA glycosylase
#2: Protein
Early protein GP1B


Mass: 6455.130 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage PZA (virus) / Gene: 1B / Production host: Escherichia coli (E. coli) / References: UniProt: P06948
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 2.46 Å3/Da / Density % sol: 49.95 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.09M Ammonium Acetate, 14.3% Peg 10K, 0.1M Bis-Tris pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2013
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.16→50 Å / Num. all: 44596 / Num. obs: 44596 / % possible obs: 99.2 % / Observed criterion σ(F): 1.14 / Observed criterion σ(I): 1.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.16-2.224.60.6422.33435199.2
12.77-504.40.0253684199.4

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
BUSTER2.10.0refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.16→50 Å / σ(F): 1.5 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2018 2986 RANDOM
Rwork0.171 --
obs0.1725 44499 -
all-44499 -
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2.16→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5196 0 60 409 5665
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg1.01
X-RAY DIFFRACTIONt_bond_d0.01
X-RAY DIFFRACTIONt_dihedral_angle_d3.2
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.4141-0.0634-0.64571.92480.49342.36470.0933-0.19550.01360.0749-0.1192-0.2876-0.02150.13550.0259-0.0854-0.0209-0.0249-0.02550.00010.032919.9604-28.991943.0575
21.9221-0.29130.11251.1295-0.07371.17170.02490.0041-0.1993-0.07590.01920.13570.0633-0.0017-0.0441-0.0877-0.0136-0.0034-0.1087-0.01090.01521.0304-32.159633.6273
302.762-2.91044.6935-2.91041.3039-0.01120.13860.1622-0.15280.0687-0.1454-0.34770.0802-0.0574-0.1731-0.0040.1484-0.20140.1520.283713.799813.7861-2.5339
42.668-0.324-0.53083.8011-0.21141.63810.14720.54280.5442-0.2499-0.06080.2372-0.2396-0.0808-0.0864-0.19530.0185-0.005-0.07550.1455-0.06224.5645-3.23875.2779
52.5521-0.1184-0.43951.8885-0.42373.1423-0.0323-0.29030.00980.19980.0906-0.06470.10040.1984-0.0582-0.0830.02090.0112-0.0585-0.0265-0.0057-6.6305-12.992944.6483
62.6098-0.1654-0.65742.3253-0.22260.30510.06910.0071-0.0118-0.2052-0.0390.213-0.0234-0.0344-0.0301-0.0545-0.0209-0.0099-0.0687-0.01530.0334-16.5261-6.847235.6307
71.8923-0.7692-0.30341.08740.25313.5436-0.10680.46280.2761-0.0987-0.0129-0.1066-0.19070.14880.1197-0.0546-0.05280.0427-0.01320.0119-0.011125.553-10.187513.7779
81.1560.02950.05242.57811.73073.2897-0.00510.0580.0861-0.1596-0.0679-0.07970.192-0.0590.073-0.0581-0.01880.0137-0.0318-0.00890.021422.0271-16.365427.0825
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|16 - 60}A16 - 60
2X-RAY DIFFRACTION2{A|61 - 244}A61 - 244
3X-RAY DIFFRACTION3{B|18 - 60}B18 - 60
4X-RAY DIFFRACTION4{B|61 - 244}B61 - 244
5X-RAY DIFFRACTION5{C|7 - 55}C7 - 55
6X-RAY DIFFRACTION6{D|8 - 55}D8 - 55
7X-RAY DIFFRACTION7{E|9 - 55}E9 - 55
8X-RAY DIFFRACTION8{F|8 - 55}F8 - 55

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