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- PDB-3jxz: Bacillus cereus Alkylpurine DNA Glycosylase AlkD Bound to DNA Con... -

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Basic information

Entry
Database: PDB / ID: 3jxz
TitleBacillus cereus Alkylpurine DNA Glycosylase AlkD Bound to DNA Containing an Abasic Site (across from T)
Components
  • DNA (5'-D(*AP*AP*AP*GP*CP*CP*TP*CP*CP*C)-3')
  • DNA (5'-D(*TP*GP*GP*GP*(3DR)P*GP*GP*CP*TP*T)-3')
  • alkylpurine DNA glycosylase AlkD
Keywordshydrolase/DNA / HEAT repeat / DNA binding / DNA glycosylase / DNA alkylation / lyase-DNA COMPLEX / hydrolase-DNA COMPLEX
Function / homologyLeucine-rich Repeat Variant - #90 / DNA alkylation repair enzyme / DNA alkylation repair enzyme / Leucine-rich Repeat Variant / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha / DNA / DNA alkylation repair protein
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsRubinson, E.H. / Eichman, B.F.
CitationJournal: Nature / Year: 2010
Title: An unprecedented nucleic acid capture mechanism for excision of DNA damage.
Authors: Rubinson, E.H. / Gowda, A.S. / Spratt, T.E. / Gold, B. / Eichman, B.F.
History
DepositionSep 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq
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.db_align_beg / _struct_ref_seq.db_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: alkylpurine DNA glycosylase AlkD
B: DNA (5'-D(*TP*GP*GP*GP*(3DR)P*GP*GP*CP*TP*T)-3')
C: DNA (5'-D(*AP*AP*AP*GP*CP*CP*TP*CP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)32,9273
Polymers32,9273
Non-polymers00
Water4,954275
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-16 kcal/mol
Surface area13560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.333, 57.445, 53.655
Angle α, β, γ (deg.)90.00, 101.88, 90.00
Int Tables number4
Space group name H-MP1211
Detailsbiological unit = asymmetric unit

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Components

#1: Protein alkylpurine DNA glycosylase AlkD


Mass: 26970.260 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 10987 / Gene: AlkD, BC_4913 / Plasmid: pBG103 / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 / References: UniProt: Q816E8
#2: DNA chain DNA (5'-D(*TP*GP*GP*GP*(3DR)P*GP*GP*CP*TP*T)-3')


Mass: 2982.927 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*AP*AP*AP*GP*CP*CP*TP*CP*CP*C)-3')


Mass: 2973.971 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.4 Å3/Da / Density % sol: 48.68 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: .1 M BisTris pH 6.5 .1 M NaCl, 19% PEG 3350, 2% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9785 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 12, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.75→28.9 Å / Num. all: 31562 / Num. obs: 30136 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 22.4 Å2 / Rsym value: 0.056 / Net I/σ(I): 13.5
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 2868 / Rsym value: 0.467 / % possible all: 94.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 3BVS

3bvs


Resolution: 1.75→28.867 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2247 1527 5.07 %random
Rwork0.1845 ---
all0.2033 30137 --
obs0.1866 30134 95.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.383 Å2 / ksol: 0.388 e/Å3
Displacement parametersBiso mean: 32.42 Å2
Refinement stepCycle: LAST / Resolution: 1.75→28.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1893 394 0 275 2562
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062400
X-RAY DIFFRACTIONf_angle_d1.0293329
X-RAY DIFFRACTIONf_dihedral_angle_d20.626915
X-RAY DIFFRACTIONf_chiral_restr0.07359
X-RAY DIFFRACTIONf_plane_restr0.005351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.80650.34551230.3532584X-RAY DIFFRACTION95
1.8065-1.8710.33371480.31162585X-RAY DIFFRACTION96
1.871-1.94590.33731310.26472568X-RAY DIFFRACTION96
1.9459-2.03450.32561270.23022601X-RAY DIFFRACTION96
2.0345-2.14170.26431450.20042612X-RAY DIFFRACTION96
2.1417-2.27580.24351400.17382583X-RAY DIFFRACTION96
2.2758-2.45150.20441420.16652586X-RAY DIFFRACTION96
2.4515-2.6980.22111580.16492618X-RAY DIFFRACTION97
2.698-3.0880.23511270.16822624X-RAY DIFFRACTION96
3.088-3.88910.17851400.14872610X-RAY DIFFRACTION95
3.8891-28.87050.1821460.16282636X-RAY DIFFRACTION94
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined0.22710.0825-0.0860.91510.11270.45780.0405-0.03370.00370.0651-0.06290.1209-0.0102-0.06550.01660.15170.0010.00580.16910.00130.14355.6045-17.3672-5.3577
2-0.93541.1924-0.43050.48710.16721.49060.06260.3328-0.1020.2056-0.13630.25750.1867-0.26040.05410.24880.03160.04010.258-0.00570.3318
30.7583-0.3088-0.65320.04940.3176-0.00320.09060.38850.03980.1175-0.12040.2369-0.012-0.21510.09310.22290.0680.00970.3611-0.02930.3258
Refinement TLS groupSelection details: CHAIN C

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