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- PDB-3tr7: Structure of a uracil-DNA glycosylase (ung) from Coxiella burnetii -

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Basic information

Entry
Database: PDB / ID: 3tr7
TitleStructure of a uracil-DNA glycosylase (ung) from Coxiella burnetii
ComponentsUracil-DNA glycosylase
KeywordsHYDROLASE / DNA metabolism
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
Uracil-DNA glycosylase
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1958 Å
AuthorsCheung, J. / Franklin, M.C. / Rudolph, M. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J.
CitationJournal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.
History
DepositionSep 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Jan 20, 2016Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uracil-DNA glycosylase


Theoretical massNumber of molelcules
Total (without water)26,1161
Polymers26,1161
Non-polymers00
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.175, 54.633, 76.762
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uracil-DNA glycosylase / UDG


Mass: 26116.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA493 / Gene: CBU_0988, ung / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83CW4, uracil-DNA glycosylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
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: 42.38 %
Crystal growTemperature: 295 K / Method: sitting drop / pH: 7.5
Details: 30% PEG 1500, pH 7.5, sitting drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: May 13, 2011
RadiationMonochromator: VARIMAX HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.195→30 Å / Num. all: 11927 / Num. obs: 11784 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.07 / Χ2: 1.049 / Net I/σ(I): 8.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.195-2.242.80.3515241.155191
2.24-2.282.90.3215661.943197.1
2.28-2.323.50.2355790.9199
2.32-2.3740.2435750.937199.5
2.37-2.424.10.2075890.893199.5
2.42-2.484.10.175880.823199.2
2.48-2.544.10.1585770.832199.5
2.54-2.614.10.1695720.777199.1
2.61-2.684.20.135890.777199.7
2.68-2.774.20.1245840.914198.8
2.77-2.874.10.1095720.854199.5
2.87-2.994.30.0915860.862199.2
2.99-3.124.30.0785940.883199.5
3.12-3.294.20.0666000.9011100
3.29-3.494.20.0556041.052199.8
3.49-3.764.30.0565891.3391100
3.76-4.144.30.0496041.2181100
4.14-4.734.20.0446151.171199.8
4.73-5.964.20.0476241.253199.7
5.96-303.80.0476531.824197

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1958→21.856 Å / Occupancy max: 1 / Occupancy min: 0.37 / FOM work R set: 0.8052 / SU ML: 0.59 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2368 558 4.76 %RANDOM
Rwork0.1889 ---
all0.1912 11894 --
obs0.1912 11727 98.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.605 Å2 / ksol: 0.327 e/Å3
Displacement parametersBiso max: 89.4 Å2 / Biso mean: 29.5623 Å2 / Biso min: 10.32 Å2
Baniso -1Baniso -2Baniso -3
1--1.7357 Å20 Å2-0 Å2
2--3.7165 Å2-0 Å2
3----1.9808 Å2
Refinement stepCycle: LAST / Resolution: 2.1958→21.856 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1741 0 0 197 1938
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021813
X-RAY DIFFRACTIONf_angle_d0.5472464
X-RAY DIFFRACTIONf_chiral_restr0.039261
X-RAY DIFFRACTIONf_plane_restr0.002322
X-RAY DIFFRACTIONf_dihedral_angle_d11.912673
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1958-2.41650.34021360.25452659279596
2.4165-2.76560.26451370.2142766290399
2.7656-3.4820.24581360.181328222958100
3.482-21.85680.19531490.167729223071100
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)
12.487-0.48120.10182.1556-1.60224.3340.06420.41370.032-0.4051-0.1454-0.16740.4741-0.18230.06960.24910.0680.04330.2463-0.00770.297823.596612.5176-6.209
20.64780.14390.32420.25830.21432.69920.02240.1253-0.03320.0018-0.066-0.1673-0.36560.32940.02520.2092-0.00130.02230.23680.01210.233228.236627.11953.7624
31.27660.253-0.55250.34560.14832.25670.03820.0257-0.0090.0118-0.02590.0134-0.1751-0.02480.00540.19370.0268-0.01920.17120.00230.20419.432724.02649.7756
43.31891.2471-0.12893.62591.60273.5262-0.10040.35240.3229-0.5353-0.03390.4275-0.2388-0.24960.14060.21110.0197-0.00690.25840.04190.27627.697720.29522.6389
52.70850.3010.05250.7356-0.61763.80.07090.23510.27050.31020.24670.0307-0.5661-0.6537-0.19250.25780.0680.02730.2908-0.02120.2098.158928.965516.2356
62.95110.297-0.63054.15550.40532.7313-0.0135-0.1284-0.32480.2987-0.04450.25120.365-0.25940.01510.209-0.00130.01910.24230.01330.226713.673313.151619.1683
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 7:20)A0
2X-RAY DIFFRACTION2chain 'A' and (resseq 21:89)A0
3X-RAY DIFFRACTION3chain 'A' and (resseq 90:167)A0
4X-RAY DIFFRACTION4chain 'A' and (resseq 168:182)A0
5X-RAY DIFFRACTION5chain 'A' and (resseq 183:203)A0
6X-RAY DIFFRACTION6chain 'A' and (resseq 204:225)A0

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