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

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Basic information

Entry
Database: PDB / ID: 3rzm
TitleDuplex Interrogation by a Direct DNA Repair Protein in the Search of Damage
Components
  • 5'-D(*AP*TP*GP*TP*AP*TP*AP*AP*CP*TP*GP*CP*G)-3'
  • 5'-D(*TP*CP*GP*CP*AP*GP*TP*TP*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: 3.06 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 1.1Jul 3, 2013Group: Database references
Revision 1.2Nov 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_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 1.3Nov 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*AP*AP*CP*TP*GP*CP*G)-3'
C: 5'-D(*TP*CP*GP*CP*AP*GP*TP*TP*AP*TP*AP*CP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4644
Polymers31,3883
Non-polymers761
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-8 kcal/mol
Surface area13440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.050, 75.050, 169.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 23446.746 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 56-260 / 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*AP*AP*CP*TP*GP*CP*G)-3'


Mass: 3990.622 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(*TP*CP*GP*CP*AP*GP*TP*TP*AP*TP*AP*CP*A)-3'


Mass: 3950.598 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-XL3 / propane-1-thiol


Mass: 76.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8S
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: 3.81 Å3/Da / Density % sol: 67.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12% PEG 4000, 0.1M SODIUM CHLORIDE, 0.05M magnesium chloride, 0.1M cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.54 Å
DetectorDate: Apr 17, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.06→50 Å / Num. all: 9740 / Num. obs: 9613 / % possible obs: 98.7 % / Observed criterion σ(F): 2.2 / Observed criterion σ(I): 1
Reflection shellResolution: 3.06→3.17 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BTX

3btx


Resolution: 3.06→50 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.873 / SU B: 32.402 / SU ML: 0.362 / Cross valid method: THROUGHOUT / σ(F): 2.2 / ESU R Free: 0.434 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28887 469 4.8 %RANDOM
Rwork0.25252 ---
all0.25415 9273 --
obs0.25415 9236 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 84.353 Å2
Baniso -1Baniso -2Baniso -3
1--1.06 Å20 Å20 Å2
2---1.06 Å20 Å2
3---2.12 Å2
Refinement stepCycle: LAST / Resolution: 3.06→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1614 527 4 0 2145
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0212258
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2552.2423165
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8095199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.16121.64679
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.99315274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6981517
X-RAY DIFFRACTIONr_chiral_restr0.0740.2345
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211545
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_it0.4311.51002
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.80121617
X-RAY DIFFRACTIONr_scbond_it0.87431256
X-RAY DIFFRACTIONr_scangle_it1.6284.51548
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.06→3.139 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 44 -
Rwork0.386 657 -
obs--98.59 %
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)
14.04511.0015-1.36584.60161.08361.383-0.1203-0.2243-0.13780.41210.1584-0.07170.14990.2014-0.03820.49840.05420.04470.03740.03770.110221.8171-1.803818.2493
20000000000000000.2737000.273700.273740.3297.71625.436
30000000000000000.2737000.273700.273740.227.54723.407
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A55 - 260
2X-RAY DIFFRACTION2B261 - 273
3X-RAY DIFFRACTION3C274 - 286

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