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- PDB-6lyv: The crystal structure of SAUGI/KSHVUDG complex -

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Basic information

Entry
Database: PDB / ID: 6lyv
TitleThe crystal structure of SAUGI/KSHVUDG complex
Components
  • SAUGI
  • Uracil-DNA glycosylase
KeywordsHYDROLASE / DNA mimic protein / uracil-DNA glycosylase inhibitor / uracil-DNA glycosylase / DNA repair / herpesvirus
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 / metal ion binding
Similarity search - Function
S. aureus uracil DNA glycosylase inhibitor / Uracil DNA glycosylase inhibitor superfamily / S. aureus uracil DNA glycosylase inhibitor / S. aureus uracil DNA glycosylase inhibitor / 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 ...S. aureus uracil DNA glycosylase inhibitor / Uracil DNA glycosylase inhibitor superfamily / S. aureus uracil DNA glycosylase inhibitor / S. aureus uracil DNA glycosylase inhibitor / 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 / Nuclear Transport Factor 2; Chain: A, / Roll / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uracil-DNA glycosylase / Core gene UL2 family protein / Uncharacterized protein
Similarity search - Component
Biological speciesHuman herpesvirus 8
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLiao, Y.T. / Ko, T.P. / Wang, H.C.
Funding support Taiwan, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)103-2311-B-038-005-MY3 Taiwan
Ministry of Science and Technology (MoST, Taiwan)106-2311-B-038-002 Taiwan
Ministry of Science and Technology (MoST, Taiwan)106-2313-B-038 -004 -MY3 Taiwan
CitationJournal: Int.J.Biol.Macromol. / Year: 2020
Title: Structural insight into the differential interactions between the DNA mimic protein SAUGI and two gamma herpesvirus uracil-DNA glycosylases.
Authors: Liao, Y.T. / Lin, S.J. / Ko, T.P. / Liu, C.Y. / Hsu, K.C. / Wang, H.C.
History
DepositionFeb 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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: SAUGI
C: Uracil-DNA glycosylase
D: SAUGI
E: Uracil-DNA glycosylase
F: SAUGI
G: Uracil-DNA glycosylase
H: SAUGI
I: Uracil-DNA glycosylase
J: SAUGI
K: Uracil-DNA glycosylase
L: SAUGI
M: Uracil-DNA glycosylase
N: SAUGI
O: Uracil-DNA glycosylase
P: SAUGI


Theoretical massNumber of molelcules
Total (without water)339,29916
Polymers339,29916
Non-polymers00
Water14,088782
1
A: Uracil-DNA glycosylase
B: SAUGI


Theoretical massNumber of molelcules
Total (without water)42,4122
Polymers42,4122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-9 kcal/mol
Surface area15240 Å2
MethodPISA
2
C: Uracil-DNA glycosylase
D: SAUGI


Theoretical massNumber of molelcules
Total (without water)42,4122
Polymers42,4122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-9 kcal/mol
Surface area15020 Å2
MethodPISA
3
E: Uracil-DNA glycosylase
F: SAUGI


Theoretical massNumber of molelcules
Total (without water)42,4122
Polymers42,4122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-10 kcal/mol
Surface area14780 Å2
MethodPISA
4
G: Uracil-DNA glycosylase
H: SAUGI


Theoretical massNumber of molelcules
Total (without water)42,4122
Polymers42,4122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-11 kcal/mol
Surface area14940 Å2
MethodPISA
5
I: Uracil-DNA glycosylase
J: SAUGI


Theoretical massNumber of molelcules
Total (without water)42,4122
Polymers42,4122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-10 kcal/mol
Surface area14900 Å2
MethodPISA
6
K: Uracil-DNA glycosylase
L: SAUGI


Theoretical massNumber of molelcules
Total (without water)42,4122
Polymers42,4122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-11 kcal/mol
Surface area15020 Å2
MethodPISA
7
M: Uracil-DNA glycosylase
N: SAUGI


Theoretical massNumber of molelcules
Total (without water)42,4122
Polymers42,4122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-12 kcal/mol
Surface area14480 Å2
MethodPISA
8
O: Uracil-DNA glycosylase
P: SAUGI


Theoretical massNumber of molelcules
Total (without water)42,4122
Polymers42,4122
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-13 kcal/mol
Surface area15260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.887, 92.196, 98.107
Angle α, β, γ (deg.)108.141, 90.612, 92.229
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
12
22
32
42
52
62
72
82

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPLEULEU(chain 'A' and resid 5 through 236)AA5 - 23622 - 253
221ASPASPLEULEU(chain 'C' and resid 5 through 236)CC5 - 23622 - 253
331ASPASPLEULEU(chain 'E' and resid 5 through 236)EE5 - 23622 - 253
441ASPASPLEULEU(chain 'G' and resid 5 through 236)GG5 - 23622 - 253
551ASPASPLEULEU(chain 'I' and resid 5 through 236)II5 - 23622 - 253
661ASPASPLEULEU(chain 'K' and resid 5 through 236)KK5 - 23622 - 253
771ASPASPLEULEU(chain 'M' and resid 5 through 236)MM5 - 23622 - 253
881ASPASPLEULEU(chain 'O' and resid 5 through 236)OO5 - 23622 - 253
192METMETTHRTHR(chain 'B' and resid 1 through 97)BB1 - 971 - 97
2102METMETTHRTHR(chain 'D' and resid 1 through 97)DD1 - 971 - 97
3112METMETTHRTHRchain 'F'FF1 - 971 - 97
4122METMETTHRTHR(chain 'H' and resid 1 through 97)HH1 - 971 - 97
5132METMETTHRTHR(chain 'J' and resid 1 through 97)JJ1 - 971 - 97
6142METMETTHRTHR(chain 'L' and resid 1 through 97)LL1 - 971 - 97
7152METMETTHRTHRchain 'N'NN1 - 971 - 97
8162METMETTHRTHR(chain 'P' and resid 1 through 97)PP1 - 971 - 97

NCS ensembles :
ID
1
2

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Components

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


Mass: 29045.283 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 8 / Gene: ORF46 / Production host: Escherichia coli (E. coli)
References: UniProt: Q76RG8, UniProt: F5HFA1*PLUS, uracil-DNA glycosylase
#2: Protein
SAUGI


Mass: 13367.123 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q936H5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 782 / 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: 2.17 Å3/Da / Density % sol: 43.41 %
Crystal growTemperature: 293 K / Method: evaporation / Details: tri-Ammonium citrate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 74977 / % possible obs: 96.2 % / Redundancy: 1.8 % / Biso Wilson estimate: 41.54 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 7.5
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.437 / Num. unique obs: 7580

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AYS

5ays


Resolution: 2.7→19.96 Å / SU ML: 0.3511 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 24.4378
RfactorNum. reflection% reflection
Rfree0.2315 3674 4.99 %
Rwork0.1918 --
obs0.1938 73649 93.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 46.05 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21737 0 0 782 22519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003422341
X-RAY DIFFRACTIONf_angle_d0.596730392
X-RAY DIFFRACTIONf_chiral_restr0.04363339
X-RAY DIFFRACTIONf_plane_restr0.00453844
X-RAY DIFFRACTIONf_dihedral_angle_d18.65968155
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.730.30691030.25621759X-RAY DIFFRACTION62.19
2.73-2.770.33691150.25182509X-RAY DIFFRACTION86.29
2.77-2.810.29441240.26352623X-RAY DIFFRACTION90.33
2.81-2.850.29631400.26082688X-RAY DIFFRACTION94.11
2.85-2.90.31721530.25872691X-RAY DIFFRACTION95.37
2.9-2.940.31381360.2442852X-RAY DIFFRACTION97.39
2.94-2.990.29791520.24222752X-RAY DIFFRACTION97.42
2.99-3.050.28171530.24132796X-RAY DIFFRACTION97.58
3.05-3.110.31251750.24082749X-RAY DIFFRACTION97.05
3.11-3.170.28481280.23292823X-RAY DIFFRACTION96.88
3.17-3.240.29631120.21662786X-RAY DIFFRACTION97.61
3.24-3.310.26411540.21152811X-RAY DIFFRACTION97.12
3.31-3.40.22651670.20772756X-RAY DIFFRACTION97.21
3.4-3.490.29671320.19272802X-RAY DIFFRACTION97.02
3.49-3.590.20711320.19042794X-RAY DIFFRACTION96.86
3.59-3.70.22671370.19112773X-RAY DIFFRACTION96.01
3.7-3.840.24621560.18762733X-RAY DIFFRACTION95.79
3.84-3.990.21961350.1742773X-RAY DIFFRACTION96.16
3.99-4.170.20191390.16232741X-RAY DIFFRACTION96.1
4.17-4.390.18781250.15672767X-RAY DIFFRACTION95.54
4.39-4.660.19461430.15272726X-RAY DIFFRACTION95.19
4.66-5.010.17761670.15672683X-RAY DIFFRACTION94.53
5.01-5.510.19721450.17162678X-RAY DIFFRACTION93.57
5.51-6.280.2331630.18612631X-RAY DIFFRACTION92.82
6.28-7.830.19641430.18182640X-RAY DIFFRACTION91.97
7.83-19.960.16131450.15612639X-RAY DIFFRACTION92.15

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