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- PDB-4uqm: Crystal structure determination of uracil-DNA N-glycosylase (UNG)... -

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Basic information

Entry
Database: PDB / ID: 4uqm
TitleCrystal structure determination of uracil-DNA N-glycosylase (UNG) from Deinococcus radiodurans in complex with DNA - new insights into the role of the Leucine-loop for damage recognition and repair
Components
  • 5'-D(*CP*CP*TP*AP*TP*CP*CP*AP*AAB*GP*TP*CP*TP*CP*CP*G)-3'
  • 5'-D(*GP*CP*GP*GP*AP*GP*AP*CP*AP*TP*GP*GP*AP*CP*AP*G)-3'
  • URACIL-DNA GLYCOSYLASE
KeywordsHYDROLASE/DNA / HYDROLASE-DNA COMPLEX / BASE EXCISION REPAIR / RADIATION RESISTANCE / DNA DAMAGE / DNA REPAIR / PROTEIN-DNA 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
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 ...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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Uracil-DNA glycosylase
Similarity search - Component
Biological speciesDEINOCOCCUS RADIODURANS (radioresistant)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsPedersen, H.L. / Johnson, K.A. / McVey, C.E. / Leiros, I. / Moe, E.
CitationJournal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2015
Title: Structure determination of uracil-DNA N-glycosylase from Deinococcus radiodurans in complex with DNA.
Authors: Pedersen, H.L. / Johnson, K.A. / McVey, C.E. / Leiros, I. / Moe, E.
History
DepositionJun 24, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Sep 27, 2017Group: Advisory / Data collection / Category: diffrn_detector / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_detector.type
Revision 1.3Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Jan 10, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _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: 5'-D(*CP*CP*TP*AP*TP*CP*CP*AP*AAB*GP*TP*CP*TP*CP*CP*G)-3'
C: 5'-D(*GP*CP*GP*GP*AP*GP*AP*CP*AP*TP*GP*GP*AP*CP*AP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5965
Polymers37,4693
Non-polymers1282
Water4,324240
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-17.1 kcal/mol
Surface area13220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.300, 98.720, 43.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein URACIL-DNA GLYCOSYLASE / UDG / URACIL DNA GLYCOSYLASE


Mass: 27794.527 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: RESIDUES 1-15 AND 246-247 NOT VISIBLE IN ELECTRON DENSITY
Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RWH9, uracil-DNA glycosylase

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain 5'-D(*CP*CP*TP*AP*TP*CP*CP*AP*AAB*GP*TP*CP*TP*CP*CP*G)-3'


Mass: 4677.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: NUCLEOTIDE 9 IS ABASIC / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain 5'-D(*GP*CP*GP*GP*AP*GP*AP*CP*AP*TP*GP*GP*AP*CP*AP*G)-3'


Mass: 4997.255 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 3 types, 242 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.51 Å3/Da / Density % sol: 56.28 % / Description: NONE
Crystal growpH: 4.6 / Details: 0.05M NACITRATE, PH4.6 20%(W/V) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→30 Å / Num. obs: 78013 / % possible obs: 95.7 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 13
Reflection shellResolution: 1.35→1.38 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.15 / % possible all: 91.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BOO

2boo


Resolution: 1.35→27.03 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.032 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES WITH TLS ADDED TERMINAL DNA NUCLEOTIDES HAD HIGH B-FACTORS, BUT WERE VISIBLE IN ELECTRON DENSITY CONTOURED AT LOW SIGMA LEVEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.21083 3916 5 %RANDOM
Rwork0.18241 ---
obs0.1838 74096 95.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Refinement stepCycle: LAST / Resolution: 1.35→27.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1829 457 7 240 2533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0172465
X-RAY DIFFRACTIONr_bond_other_d0.0020.022101
X-RAY DIFFRACTIONr_angle_refined_deg1.7191.7743445
X-RAY DIFFRACTIONr_angle_other_deg1.17534862
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0155.789247
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24523.29588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.40515304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3691513
X-RAY DIFFRACTIONr_chiral_restr0.240.2351
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212439
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02573
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9781.143921
X-RAY DIFFRACTIONr_mcbond_other0.977920
X-RAY DIFFRACTIONr_mcangle_it1.0881.7171151
X-RAY DIFFRACTIONr_mcangle_other1.0872.5681152
X-RAY DIFFRACTIONr_scbond_it1.4621.2881544
X-RAY DIFFRACTIONr_scbond_other1.4621.2891544
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5831.9062292
X-RAY DIFFRACTIONr_long_range_B_refined1.7684468
X-RAY DIFFRACTIONr_long_range_B_other1.6834352
X-RAY DIFFRACTIONr_rigid_bond_restr8.99932437
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded4.29752323
LS refinement shellResolution: 1.349→1.384 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 277 -
Rwork0.29 5188 -
obs--91.63 %
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)
11.6445-0.17290.54021.6296-0.68273.5554-0.083-0.1313-0.24730.0580.02350.27410.247-0.38250.05950.1048-0.06070.00880.1097-0.00250.168-7.1363-40.5995-5.4474
20.8418-0.0046-0.23671.41350.53362.596-0.0134-0.0702-0.07950.0548-0.03120.1036-0.0095-0.16350.04470.0051-0.00650.00090.06560.00320.05720.4818-29.2877-3.646
33.3297-0.1880.45173.9907-1.73752.85880.04020.02990.21360.0137-0.07820.2094-0.3112-0.17490.0380.08580.01240.00170.0781-0.01770.03882.3915-18.2943-13.1172
41.8048-1.0862-0.35132.13761.31835.44550.07320.1250.1287-0.2228-0.0014-0.2443-0.33710.2228-0.07190.0856-0.04840.01670.09870.02310.062413.4716-19.4303-20.4948
51.020.29710.04912.1961-1.04393.0861-0.01970.13290.0346-0.16710.00840.1416-0.1783-0.08240.01130.05840.004-0.00310.069-0.0130.03073.7173-23.9029-21.7307
61.1291-0.0829-0.26371.59540.24061.7942-0.0262-0.0414-0.2060.03220.0215-0.10140.28730.15840.00470.05030.01220.00070.05860.00630.082310.0099-36.3683-9.7041
71.7214-0.12740.64521.70360.26372.41930.07840.1547-0.1178-0.2448-0.0275-0.09950.05780.1836-0.0510.0777-0.00370.03350.10260.00380.044311.9063-28.3589-24.0581
80.01710.11090.12350.90760.9941.09650.0441-0.02120.0278-0.024-0.0417-0.0695-0.0675-0.089-0.00230.3354-0.0622-0.01110.2667-0.04350.418618.6335-8.107-3.615
97.2369-2.55564.12590.9096-1.44762.37250.1697-0.072-0.327-0.02770.01750.09510.1585-0.0488-0.18720.1938-0.0274-0.03970.1815-0.00850.179328.1265-29.1384-2.1033
103.3407-1.19120.87433.71831.88792.20370.03630.04680.0449-0.12910.01510.3302-0.0262-0.1611-0.05140.0218-0.0391-0.0210.23730.02370.258425.1618-19.9122-2.3512
1100000000000000-00.132000.13200.132000
1200000000000000-00.132000.13200.132000
1300000000000000-00.132000.13200.132000
1400000000000000-00.132000.13200.132000
1500000000000000-00.132000.13200.132000
1600000000000000-00.132000.13200.132000
1710.81560.7251-2.2550.0581-0.12610.5378-0.0482-0.1839-0.2261-0.0221-0.0031-0.0154-0.02910.04940.05130.1225-0.02160.00550.1141-0.00710.088212.0405-21.3796-7.3332
1800000000000000-00.132000.13200.132000
1900000000000000-00.132000.13200.132000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 37
2X-RAY DIFFRACTION2A38 - 91
3X-RAY DIFFRACTION3A92 - 105
4X-RAY DIFFRACTION4A106 - 118
5X-RAY DIFFRACTION5A119 - 142
6X-RAY DIFFRACTION6A143 - 208
7X-RAY DIFFRACTION7A209 - 244
8X-RAY DIFFRACTION8B4 - 8
9X-RAY DIFFRACTION9B10 - 15
10X-RAY DIFFRACTION10C2 - 12
11X-RAY DIFFRACTION11A16 - 96
12X-RAY DIFFRACTION12A97 - 129
13X-RAY DIFFRACTION13A130 - 140
14X-RAY DIFFRACTION14A141 - 219
15X-RAY DIFFRACTION15A220 - 244
16X-RAY DIFFRACTION16B4 - 7
17X-RAY DIFFRACTION17B8 - 15
18X-RAY DIFFRACTION18C3 - 8
19X-RAY DIFFRACTION19C9 - 12

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