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- PDB-9iro: Crystal structure of SeUGI and SAUDG -

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Basic information

Entry
Database: PDB / ID: 9iro
TitleCrystal structure of SeUGI and SAUDG
Components
  • Staphylococcus epidermidis uracil-DNA glycosylase inhibitor (SeUGI)
  • Uracil-DNA glycosylase
KeywordsDNA BINDING PROTEIN/INHIBITOR / DNA mimic protein / uracil-DNA glycosylase / uracil-DNA glycosylase inhibitor / DNA BINDING PROTEIN / DNA BINDING PROTEIN-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 / cytoplasm
Similarity search - Function
S. aureus uracil DNA glycosylase inhibitor / Uracil DNA glycosylase inhibitor superfamily / 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-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily
Similarity search - Domain/homology
Uncharacterized protein / Uracil-DNA glycosylase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Staphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsWang, H.C. / Ko, T.P.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)NSTC 112-2628-B-038 -011 Taiwan
CitationJournal: To Be Published
Title: Establish a Least-Square Circle Feature Extraction method for identifying new DNA mimic proteins
Authors: Liao, B.C. / Chen, Y.H. / Chou, H.H. / Hsu, K.C. / Ko, T.P. / Liu, C.Y. / Lin, S.J. / Chen, Y.C. / Hsieh, S.Y. / Wang, H.C.
History
DepositionJul 16, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uracil-DNA glycosylase
B: Staphylococcus epidermidis uracil-DNA glycosylase inhibitor (SeUGI)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8473
Polymers41,7512
Non-polymers961
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-20 kcal/mol
Surface area15960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.895, 75.860, 77.056
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Uracil-DNA glycosylase / UDG


Mass: 26071.443 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: ung, SAR0586 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6GJ88, uracil-DNA glycosylase
#2: Protein Staphylococcus epidermidis uracil-DNA glycosylase inhibitor (SeUGI)


Mass: 15679.446 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus epidermidis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A169SZN4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 42.29 %
Crystal growTemperature: 298.15 K / Method: evaporation / Details: 1.5 M ammonium sulfate, 0.1 M Tris, pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Oct 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.18→30 Å / Num. obs: 19056 / % possible obs: 98.7 % / Redundancy: 5.6 % / Biso Wilson estimate: 33.79 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 30.1
Reflection shellResolution: 2.18→2.26 Å / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 6.9 / Num. unique obs: 1848

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Processing

Software
NameVersionClassification
HKL-2000data scaling
MOLREPphasing
BUCCANEERmodel building
PHENIX1.19.2_4158refinement
HKL-2000data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WDG

3wdg


Resolution: 2.18→24.71 Å / SU ML: 0.2302 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.1029
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2389 947 4.98 %
Rwork0.1915 18061 -
obs0.1938 19008 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.49 Å2
Refinement stepCycle: LAST / Resolution: 2.18→24.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2783 0 5 197 2985
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022866
X-RAY DIFFRACTIONf_angle_d0.48653892
X-RAY DIFFRACTIONf_chiral_restr0.0416418
X-RAY DIFFRACTIONf_plane_restr0.0033498
X-RAY DIFFRACTIONf_dihedral_angle_d14.38631046
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.290.33081310.29922455X-RAY DIFFRACTION96.35
2.29-2.430.29811340.2322595X-RAY DIFFRACTION99.96
2.43-2.620.24331350.21832565X-RAY DIFFRACTION100
2.62-2.890.24571340.22132592X-RAY DIFFRACTION100
2.89-3.30.24341370.1992600X-RAY DIFFRACTION99.82
3.3-4.160.22251310.16822513X-RAY DIFFRACTION95.07
4.16-24.710.21371450.16322741X-RAY DIFFRACTION99.18
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)
12.21306190149-0.173743002618-1.104794541280.01931660976130.1328564867870.6074493064930.0138545666864-1.23056682874-0.913110166790.3473918319350.4940106192760.2259248089240.9145391332980.6312218036090.2334602802880.5425058800780.0955546291366-0.1302827310310.3524621690720.08423440691370.43959324246915.6749122254-41.610882590718.3428674901
20.307715169832-0.2760244096560.2577696534280.8448998817740.3244496088530.6771094151620.210874630030.000696604918734-0.377953926127-0.07579888827460.344222984568-0.7409439725540.9818307831841.287603577160.07593868648640.4899055392480.315203564125-0.1224898101430.730633469771-0.1237796661540.4591276131621.659402656-41.75602820210.291284847232
30.131634480199-0.101882372553-0.6678407195710.449537166552-0.09592235714953.706110235420.2020928945760.1721438666110.2830390048580.154523935444-0.0992373005987-0.844713629984-0.4675017973571.61742574423-0.02920292697720.2217977523190.02180986514030.03916263859170.400164814421-0.006914678352660.29494374969816.9202253127-29.49897682514.49088409139
41.80719400544-1.540286596820.1733632298012.49507005951.03150870721.164231239330.0202382257438-0.0318330729495-0.1011228016520.01734712243370.09568847620810.0670020901666-0.1455123162290.1092379275640.001569915766470.263689390933-0.0842435445947-0.01404399553620.2189088761330.05431923923490.2216956777056.97556803921-29.29136204637.97180974744
50.92317652354-0.2027418115550.947152129252.46331398758-0.3150665854991.21962654136-0.3052201679630.5139392608110.41978034268-0.02781952184970.06476191653730.0141490933491-0.320095141771-0.268350145063-0.0009006221763260.2934093545430.00570502065989-0.01051398144640.2579261339660.01512726334920.2658708293320.730562005664-20.32544124032.72113319532
63.88342232643-1.424532753661.27453595661.75242223901-0.6781733666072.741781426150.110663373910.08117012066790.0632671593548-0.163070959939-0.108702456001-0.0747104158275-0.0837485701937-0.01007899475830.006315380583570.227775882783-0.04649501872890.001437788979080.1139612702333.77718202251E-50.2081413313556.9507914788-27.71129816134.5094392239
72.653021800730.02407958896680.4774135335222.591630447780.2102128802672.702108953220.0394740640547-0.732464083571-0.6577675816220.2400105178010.2800962333380.4842985388610.45270555471-0.7819456950180.05115149511980.262320062524-0.0867465928710.02907302256330.3356652947850.1264047014430.323702411101-2.67472405694-35.905277941111.0522612252
80.385947016465-0.5101124220520.4629092523490.940536439474-0.7043234969220.536557549217-0.259407804688-0.792800087327-0.3449720686620.8929995848550.249724535040.149193165761-0.51502137547-1.667606029460.004517004675460.3593748037310.06295148559310.0948595646270.681787356567-0.0003280606526950.338020876939-7.3088628569-25.536763743519.9242972077
93.490217982190.01327780948931.807000203971.270107337280.5873438889682.633768844350.0144823589795-0.9207003238340.6148161279010.5805859774670.05650124983360.499170398538-0.8602937477140.20919683496-0.5161623028420.4718631494550.07850036983810.05585182970630.537447334424-0.07187556439660.328095859131-0.45652839549-20.022562162519.5324044297
100.4221742810680.01630368016730.2101843858870.3198613225250.3512753251150.464494766362-0.04661998170530.712020189632-0.7781342352060.196881294082-0.3666900544660.6118521748170.637485615224-1.112522489750.0103123041740.5065218886220.08341469529280.1067181942230.708701574147-0.1106944496120.5293541108928.08304576768-40.7067780529-25.5085604279
111.52883491575-0.262827350604-0.1242979122850.8739981760880.1501766478380.6304637341540.3036617437690.8446599097320.658525075569-0.946388713248-0.507043318034-0.40245101033-0.453519670390.356180448178-0.0137741253860.6229615954660.1934241045490.0497717896040.672067841850.06347522129560.455737678812-0.632521730131-23.7740278058-20.8790303343
124.08798702838-0.3469551007261.008268022612.844960532520.3151300129734.786431275030.2530383429180.0653231626955-0.40512484685-0.0756341559591-0.1596549163850.02379767568710.247228960527-0.2615179618670.002020993811690.2374226853530.0273620798476-0.04282323551610.319292320559-0.05189634230020.313052794652-7.24483314626-32.4091664184-9.74861140593
130.629644199997-0.272560663661-0.1622205829942.136373262260.8122162639761.175781782260.2593731244620.819263367298-0.516453741814-1.01655751631-0.4074224294140.405892683105-0.441268615569-0.5480243177580.008021051973250.5027864376540.0514007869489-0.1770613520080.557279881412-0.2258155244010.592491880804-12.8266407009-33.9791877687-18.9364204989
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 13 )AA1 - 131 - 13
22chain 'A' and (resid 14 through 29 )AA14 - 2914 - 29
33chain 'A' and (resid 30 through 45 )AA30 - 4530 - 45
44chain 'A' and (resid 46 through 67 )AA46 - 6746 - 67
55chain 'A' and (resid 68 through 94 )AA68 - 9468 - 94
66chain 'A' and (resid 95 through 133 )AA95 - 13395 - 133
77chain 'A' and (resid 134 through 194 )AA134 - 194134 - 194
88chain 'A' and (resid 195 through 205 )AA195 - 205195 - 205
99chain 'A' and (resid 206 through 216 )AA206 - 216206 - 216
1010chain 'B' and (resid -13 through -1 )BB-13 - -11 - 13
1111chain 'B' and (resid 0 through 24 )BB0 - 2414 - 38
1212chain 'B' and (resid 25 through 85 )BB25 - 8539 - 99
1313chain 'B' and (resid 86 through 109 )BB86 - 109100 - 123

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