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- PDB-3rzl: Duplex Interrogation by a Direct DNA Repair Protein in the Search... -

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Basic information

Entry
Database: PDB / ID: 3rzl
TitleDuplex Interrogation by a Direct DNA Repair Protein in the Search of Damage
Components
  • 5'-D(*AP*TP*GP*TP*AP*TP*CP*AP*CP*TP*GP*CP*G)-3'
  • 5'-D(*TP*CP*GP*CP*AP*GP*TP*IP*AP*TP*AP*CP*A)-3'
  • Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2
KeywordsOXIDOREDUCTASE/DNA / PROTEIN-DNA COMPLEX / JELLY-ROLL / DEMETHYLASE / NUCLEUS / OXIDOREDUCTASE-DNA complex
Function / homology
Function and homology information


cytosine C-5 DNA demethylase activity / ALKBH2 mediated reversal of alkylation damage / DNA oxidative demethylase / broad specificity oxidative DNA demethylase activity / rDNA binding / DNA alkylation repair / ferrous iron binding / nucleolus / nucleoplasm / nucleus
Similarity search - Function
DNA oxidative demethylase ALKBH2 / Alpha-ketoglutarate-dependent dioxygenase AlkB-like / Alpha-ketoglutarate-dependent dioxygenase AlkB-like / 2OG-Fe(II) oxygenase superfamily / Alpha-ketoglutarate-dependent dioxygenase AlkB-like superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
propane-1-thiol / DNA / DNA (> 10) / DNA oxidative demethylase ALKBH2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsYi, C. / Chen, B. / Qi, B. / Zhang, W. / Jia, G. / Zhang, L. / Li, C. / Dinner, A. / Yang, C. / He, C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Duplex interrogation by a direct DNA repair protein in search of base damage
Authors: Yi, C. / Chen, B. / Qi, B. / Zhang, W. / Jia, G. / Zhang, L. / Li, C.J. / Dinner, A.R. / Yang, C.G. / He, C.
History
DepositionMay 11, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Derived calculations
Revision 1.2Jul 3, 2013Group: Database references
Revision 1.3Nov 1, 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_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2
B: 5'-D(*AP*TP*GP*TP*AP*TP*CP*AP*CP*TP*GP*CP*G)-3'
C: 5'-D(*TP*CP*GP*CP*AP*GP*TP*IP*AP*TP*AP*CP*A)-3'
D: Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2
E: 5'-D(*AP*TP*GP*TP*AP*TP*CP*AP*CP*TP*GP*CP*G)-3'
F: 5'-D(*TP*CP*GP*CP*AP*GP*TP*IP*AP*TP*AP*CP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4498
Polymers63,2976
Non-polymers1522
Water32418
1
A: Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2
B: 5'-D(*AP*TP*GP*TP*AP*TP*CP*AP*CP*TP*GP*CP*G)-3'
C: 5'-D(*TP*CP*GP*CP*AP*GP*TP*IP*AP*TP*AP*CP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7244
Polymers31,6483
Non-polymers761
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-18 kcal/mol
Surface area12730 Å2
MethodPISA
2
D: Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2
E: 5'-D(*AP*TP*GP*TP*AP*TP*CP*AP*CP*TP*GP*CP*G)-3'
F: 5'-D(*TP*CP*GP*CP*AP*GP*TP*IP*AP*TP*AP*CP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7244
Polymers31,6483
Non-polymers761
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-18 kcal/mol
Surface area13080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.934, 65.006, 167.896
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Alpha-ketoglutarate-dependent dioxygenase alkB homolog 2 / Alkylated DNA repair protein alkB homolog 2 / Oxy DC1


Mass: 23721.105 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 56-261 / Mutation: C67S, C165S, G169C, C192S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALKBH2, ABH2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6NS38, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
#2: DNA chain 5'-D(*AP*TP*GP*TP*AP*TP*CP*AP*CP*TP*GP*CP*G)-3'


Mass: 3966.597 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain 5'-D(*TP*CP*GP*CP*AP*GP*TP*IP*AP*TP*AP*CP*A)-3'


Mass: 3960.597 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Chemical ChemComp-XL3 / propane-1-thiol


Mass: 76.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.41 Å3/Da / Density % sol: 48.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 8000, 0.1M SODIUM CHLORIDE, 0.05M magnesium chloride, 0.1M cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.54 Å
DetectorDate: Jun 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 19573 / Num. obs: 18575 / % possible obs: 94.9 % / Observed criterion σ(F): 2.1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.6→2.69 Å / % possible all: 96.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BTX

3btx


Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.898 / SU B: 32.213 / SU ML: 0.315 / Cross valid method: THROUGHOUT / σ(F): 2.1 / ESU R Free: 0.386 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28939 944 5.1 %RANDOM
Rwork0.22077 ---
all0.22412 18501 --
obs0.22412 17484 94.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.761 Å2
Baniso -1Baniso -2Baniso -3
1-3.27 Å20 Å20 Å2
2--1.62 Å20 Å2
3----4.89 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3164 1052 8 18 4242
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0214488
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7182.2436288
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1565403
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.66521.731156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.7615554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5481533
X-RAY DIFFRACTIONr_chiral_restr0.0970.2686
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213077
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.5611.51985
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.04323211
X-RAY DIFFRACTIONr_scbond_it1.37232503
X-RAY DIFFRACTIONr_scangle_it2.1134.53072
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.447 63 -
Rwork0.316 1262 -
obs--94.64 %
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)
13.0910.45240.9872.6252-0.33961.75480.06610.2116-0.104-0.2356-0.1009-0.29030.2512-0.00590.03480.08210.0187-0.00050.05810.01730.14220.469614.695933.3113
25.30161.72422.09754.2692-1.59699.95620.21440.5939-0.1505-0.68990.08160.1491.7602-0.7688-0.29590.4039-0.0803-0.01250.2636-0.01220.10734.48061.202125.8665
33.9129-0.0191-1.10434.6824-1.88445.2259-0.0821-0.39240.43380.35260.15260.06860.01540.1592-0.07050.06310.007-0.03460.2070.03680.21451.698338.51529.3775
44.19161.6746-5.013.7517-2.188912.6152-0.46710.67650.018-0.06380.68810.49021.973-1.7988-0.2210.4322-0.1669-0.04970.43950.03550.1649-13.080924.969916.461
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A55 - 258
2X-RAY DIFFRACTION2B259 - 271
3X-RAY DIFFRACTION2C272 - 284
4X-RAY DIFFRACTION3D55 - 258
5X-RAY DIFFRACTION4E259 - 271
6X-RAY DIFFRACTION4F272 - 284

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