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- PDB-3jx7: Bacillus cereus alkylpurine DNA glycosylase AlkD bound to DNA con... -

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Basic information

Entry
Database: PDB / ID: 3jx7
TitleBacillus cereus alkylpurine DNA glycosylase AlkD bound to DNA containing a 3-METHYLADENINE analog
Components
  • DNA (5'-D(*CP*CP*CP*GP*TP*TP*AP*GP*TP*CP*CP*G)-3')
  • DNA (5'-D(*CP*GP*GP*AP*CP*TP*(DZM)P*AP*CP*GP*GP*G)-3')
  • alkylpurine DNA glycosylase AlkD
KeywordsHYDROLASE/DNA / HEAT repeat / DNA binding / DNA glycosylase / DNA alkylation / lyase-DNA COMPLEX / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


Leucine-rich Repeat Variant - #90 / DNA alkylation repair enzyme / DNA alkylation repair enzyme / Leucine-rich Repeat Variant / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA alkylation repair protein
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 18, 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 / 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.db_align_beg / _struct_ref_seq.db_align_end / _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: alkylpurine DNA glycosylase AlkD
B: DNA (5'-D(*CP*GP*GP*AP*CP*TP*(DZM)P*AP*CP*GP*GP*G)-3')
C: DNA (5'-D(*CP*CP*CP*GP*TP*TP*AP*GP*TP*CP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)35,0643
Polymers35,0643
Non-polymers00
Water8,035446
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-16 kcal/mol
Surface area15220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.759, 92.966, 47.767
Angle α, β, γ (deg.)90.00, 113.01, 90.00
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is asymmetric unit

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Components

#1: Protein alkylpurine DNA glycosylase AlkD


Mass: 27724.082 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(*CP*GP*GP*AP*CP*TP*(DZM)P*AP*CP*GP*GP*G)-3')


Mass: 3725.468 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*CP*CP*CP*GP*TP*TP*AP*GP*TP*CP*CP*G)-3')


Mass: 3614.354 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 446 / 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: 2.2 Å3/Da / Density % sol: 44.11 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.17 M ammonium acetate, 0.085 M sodium acetate trihydrate pH 4.6, 25.5% PEG 4000, 15% glycerol , VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9785 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Sep 24, 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: 1.6→44 Å / Num. all: 40032 / Num. obs: 38351 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 17.5 Å2 / Rsym value: 0.051 / Net I/σ(I): 24.8
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.247 / % possible all: 75.3

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Processing

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

3bvs


Resolution: 1.6→34.755 Å / SU ML: 0.15 / σ(F): 1.38 / Phase error: 18.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1829 1918 5.01 %
Rwork0.1592 --
obs0.1604 38310 95.65 %
all-38326 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.413 Å2 / ksol: 0.395 e/Å3
Displacement parametersBiso mean: 23.9 Å2
Refinement stepCycle: LAST / Resolution: 1.6→34.755 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1956 487 0 446 2889
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062572
X-RAY DIFFRACTIONf_angle_d1.0913576
X-RAY DIFFRACTIONf_dihedral_angle_d19.666987
X-RAY DIFFRACTIONf_chiral_restr0.069385
X-RAY DIFFRACTIONf_plane_restr0.005368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5987-1.63870.2252930.20061974X-RAY DIFFRACTION73
1.6387-1.6830.22151160.18152201X-RAY DIFFRACTION82
1.683-1.73250.21291310.1672461X-RAY DIFFRACTION91
1.7325-1.78840.21941500.1662619X-RAY DIFFRACTION97
1.7884-1.85230.19051320.16082698X-RAY DIFFRACTION100
1.8523-1.92650.18351350.15462725X-RAY DIFFRACTION100
1.9265-2.01420.18621380.14882710X-RAY DIFFRACTION100
2.0142-2.12030.16871600.1462684X-RAY DIFFRACTION100
2.1203-2.25320.18121450.13912723X-RAY DIFFRACTION100
2.2532-2.42710.16961300.14692716X-RAY DIFFRACTION100
2.4271-2.67130.16831510.1542738X-RAY DIFFRACTION100
2.6713-3.05760.21261360.16042690X-RAY DIFFRACTION100
3.0576-3.85150.1661420.14622709X-RAY DIFFRACTION99
3.8515-34.76270.16861590.16362744X-RAY DIFFRACTION99
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)
1refined0.3495-0.1530.13410.23070.01650.26590.0002-0.00450.0033-0.00210.0185-0.0011-0.0064-0.0118-0.0130.0438-0.01680.00850.04680.00470.0451-1.854510.884118.5803
23.4224-0.04270.56510.0374-0.14040.8583-0.3114-0.30570.79660.00340.0912-0.13020.072-0.11430.18130.06890.0199-0.01480.1193-0.05650.21
32.41720.289-0.16580.59280.44120.4271-0.286-0.4520.6918-0.02270.14590.0775-0.00850.06240.11710.07350.0456-0.04490.1634-0.06910.2224
Refinement TLS groupSelection details: CHAIN C

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