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- PDB-4nih: Crystal structure of AlkB E136L mutant protein with cofactors bou... -

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Basic information

Entry
Database: PDB / ID: 4nih
TitleCrystal structure of AlkB E136L mutant protein with cofactors bound to dsDNA containing m6A/A
Components
  • 5'-D(*AP*AP*CP*GP*GP*TP*AP*TP*TP*AP*CP*CP*T)-3'
  • 5'-D(*TP*AP*GP*GP*TP*AP*AP*(6MA)P*AP*CP*CP*GP*T)-3'
  • Alpha-ketoglutarate-dependent dioxygenase AlkB
KeywordsOXIDOREDUCTASE/DNA / DNA/RNA direct repair / jelly-roll fold / DNA/RNA demethylation repair / Fe(II) / 2-KG / OXIDOREDUCTASE-DNA complex
Function / homology
Function and homology information


response to methyl methanesulfonate / oxidative RNA demethylation / DNA oxidative demethylase / broad specificity oxidative DNA demethylase activity / oxidative RNA demethylase activity / RNA repair / oxidative demethylation / DNA alkylation repair / dioxygenase activity / ferrous iron binding ...response to methyl methanesulfonate / oxidative RNA demethylation / DNA oxidative demethylase / broad specificity oxidative DNA demethylase activity / oxidative RNA demethylase activity / RNA repair / oxidative demethylation / DNA alkylation repair / dioxygenase activity / ferrous iron binding / DNA repair / cytoplasm / cytosol
Similarity search - Function
Alkylated DNA repair protein AlkB / 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 / : / DNA / DNA (> 10) / Alpha-ketoglutarate-dependent dioxygenase AlkB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.374 Å
AuthorsYi, C.Q. / Zhu, C.X.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Switching Demethylation Activities between AlkB Family RNA/DNA Demethylases through Exchange of Active-Site Residues.
Authors: Zhu, C. / Yi, C.
History
DepositionNov 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1May 28, 2014Group: Non-polymer description / Structure summary
Revision 1.2Sep 20, 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.conn_type_id / _struct_conn.id / _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 1.3Nov 6, 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
B: 5'-D(*TP*AP*GP*GP*TP*AP*AP*(6MA)P*AP*CP*CP*GP*T)-3'
C: 5'-D(*AP*AP*CP*GP*GP*TP*AP*TP*TP*AP*CP*CP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1326
Polymers30,8393
Non-polymers2933
Water8,503472
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-6 kcal/mol
Surface area12430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.072, 76.369, 53.178
Angle α, β, γ (deg.)90.00, 108.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alpha-ketoglutarate-dependent dioxygenase AlkB / Alkylated DNA repair protein AlkB / DNA oxidative demethylase AlkB


Mass: 22814.148 Da / Num. of mol.: 1 / Fragment: UNP residues 13-216 / Mutation: S129C/E136L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: alkB, aidD, b2212, JW2200 / Production host: Escherichia coli (E. coli) / References: UniProt: P05050, DNA oxidative demethylase

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain 5'-D(*TP*AP*GP*GP*TP*AP*AP*(6MA)P*AP*CP*CP*GP*T)-3'


Mass: 4073.779 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(*AP*AP*CP*GP*GP*TP*AP*TP*TP*AP*CP*CP*T)-3'


Mass: 3950.598 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 4 types, 475 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 472 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.57 Å3/Da / Density % sol: 52.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG4000, 0.1 M sodium chloride, 0.05 M magnesium chloride, 0.1 M cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 28, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.374→50 Å / Num. obs: 59661 / Observed criterion σ(F): 2.2 / Observed criterion σ(I): 2.2
Reflection shellResolution: 1.374→1.43 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.7.0029phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BIE

3bie


Resolution: 1.374→27.24 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.834 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18003 3178 5.1 %RANDOM
Rwork0.15881 ---
obs0.15987 59661 97.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.35 Å20 Å20.12 Å2
2---0.89 Å20 Å2
3---1.78 Å2
Refinement stepCycle: LAST / Resolution: 1.374→27.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1570 506 17 472 2565
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0172311
X-RAY DIFFRACTIONr_bond_other_d0.0020.021947
X-RAY DIFFRACTIONr_angle_refined_deg1.3371.7713258
X-RAY DIFFRACTIONr_angle_other_deg1.2534502
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3985228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.37523.41879
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.58915275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.531512
X-RAY DIFFRACTIONr_chiral_restr0.0830.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212348
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02551
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.374→1.409 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 195 -
Rwork0.3 3719 -
obs--82.73 %
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)
10.2429-0.0024-0.02280.32790.09870.05260.0015-0.00420.0171-0.01380.00320.00720.00440.0099-0.00470.0206-0.0024-0.00110.03340.00440.004521.63781.926576.309
22.13310.10750.32221.39351.7943.62850.11280.2323-0.06470.00950.07570.1046-0.17470.1556-0.18850.07560.00780.01710.0512-0.00170.105612.0255-7.530451.7774
30.5709-0.3595-0.11440.65060.12580.03080.0490.0372-0.0453-0.0229-0.0550.0109-0.012-0.00760.0060.02840.0083-0.00870.0385-0.00290.007926.798-16.125364.1388
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 213
2X-RAY DIFFRACTION2B2 - 5
3X-RAY DIFFRACTION2C10 - 13
4X-RAY DIFFRACTION3B6 - 13
5X-RAY DIFFRACTION3C1 - 9

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