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

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Basic information

Entry
Database: PDB / ID: 3rzk
TitleDuplex Interrogation by a Direct DNA Repair Protein in the Search of Damage
Components
  • 5'-D(*CP*TP*GP*TP*CP*TP*(EDA)P*AP*CP*TP*GP*CP*G)-3'
  • 5'-D(*TP*CP*GP*CP*AP*GP*TP*TP*AP*GP*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
2-OXOGLUTARIC ACID / : / propane-1-thiol / DNA / DNA (> 10) / DNA oxidative demethylase ALKBH2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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

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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(*CP*TP*GP*TP*CP*TP*(EDA)P*AP*CP*TP*GP*CP*G)-3'
C: 5'-D(*TP*CP*GP*CP*AP*GP*TP*TP*AP*GP*AP*CP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9986
Polymers31,7203
Non-polymers2773
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-14 kcal/mol
Surface area13160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.591, 78.591, 228.881
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 23778.156 Da / Num. of mol.: 1 / 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

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain 5'-D(*CP*TP*GP*TP*CP*TP*(EDA)P*AP*CP*TP*GP*CP*G)-3'


Mass: 3966.593 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(*TP*CP*GP*CP*AP*GP*TP*TP*AP*GP*AP*CP*A)-3'


Mass: 3975.611 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 4 types, 15 molecules

#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#6: Chemical ChemComp-XL3 / propane-1-thiol


Mass: 76.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 3.22 Å3/Da / Density % sol: 61.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 8% PEG 8000, 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: 21-ID-D / 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: 2.78→50 Å / Num. all: 11360 / Num. obs: 11348 / % possible obs: 99.9 % / Observed criterion σ(F): 3.4 / Observed criterion σ(I): 1
Reflection shellResolution: 2.78→2.88 Å / % possible all: 99.9

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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: 2.78→20 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.92 / SU B: 29.151 / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 3.4 / ESU R Free: 0.333 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2594 534 4.8 %RANDOM
Rwork0.22759 ---
all0.22912 10679 --
obs0.22912 10604 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.296 Å2
Baniso -1Baniso -2Baniso -3
1--1.89 Å2-0.95 Å20 Å2
2---1.89 Å20 Å2
3---2.84 Å2
Refinement stepCycle: LAST / Resolution: 2.78→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1626 527 15 12 2180
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0212275
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3592.2443186
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4395199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.18521.580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.85215276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.111518
X-RAY DIFFRACTIONr_chiral_restr0.0720.2344
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211562
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_it0.5241.51003
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.96621620
X-RAY DIFFRACTIONr_scbond_it0.8731272
X-RAY DIFFRACTIONr_scangle_it1.5334.51566
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.78→2.851 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.458 38 -
Rwork0.329 748 -
obs--99.62 %
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)
12.22520.43380.03281.1203-0.22160.74390.13990.1336-0.0604-0.0735-0.0427-0.02050.0380.0269-0.09720.01980.0246-0.0060.1312-0.00750.044418.025927.1498-2.9861
22.1571-0.68490.97790.5323-0.55230.91710.35450.0458-0.4015-0.06420.29770.07260.34480.0402-0.65220.2058-0.0221-0.16330.19830.00230.14051.41411.9394-1.7546
31.29790.50920.49150.87520.62480.48380.2184-0.0402-0.30650.02770.00470.16990.12870.0102-0.22310.16380.0081-0.09650.15940.01390.10231.868212.95190.0027
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A55 - 258
2X-RAY DIFFRACTION2B259 - 271
3X-RAY DIFFRACTION3C272 - 284

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