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- PDB-3t3y: Crystal structure of AlkB in complex with Fe(III) and 2-(3-hydrox... -

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Basic information

Entry
Database: PDB / ID: 3t3y
TitleCrystal structure of AlkB in complex with Fe(III) and 2-(3-hydroxypicolinomido)acetic acid
ComponentsAlpha-ketoglutarate-dependent dioxygenase AlkB
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Double-stranded beta-helix / Nucleic acid demethylase / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


response to methyl methanesulfonate / oxidative RNA demethylation / DNA oxidative demethylase / : / : / : / oxidative RNA demethylase activity / broad specificity oxidative DNA demethylase activity / RNA repair / DNA alkylation repair ...response to methyl methanesulfonate / oxidative RNA demethylation / DNA oxidative demethylase / : / : / : / oxidative RNA demethylase activity / broad specificity oxidative DNA demethylase activity / RNA repair / DNA alkylation repair / oxidative demethylation / DNA demethylation / dioxygenase activity / ferrous iron binding / DNA repair / cytoplasm
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
: / N-[(3-hydroxypyridin-2-yl)carbonyl]glycine / Alpha-ketoglutarate-dependent dioxygenase AlkB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.001 Å
AuthorsAik, W.S. / McDonough, M.A. / Schofield, C.J.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Dynamic combinatorial mass spectrometry leads to inhibitors of a 2-oxoglutarate-dependent nucleic Acid demethylase.
Authors: Woon, E.C. / Demetriades, M. / Bagg, E.A. / Aik, W. / Krylova, S.M. / Ma, J.H. / Chan, M. / Walport, L.J. / Wegman, D.W. / Dack, K.N. / McDonough, M.A. / Krylov, S.N. / Schofield, C.J.
History
DepositionJul 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 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.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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1973
Polymers22,9451
Non-polymers2522
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.813, 38.594, 40.487
Angle α, β, γ (deg.)71.250, 72.210, 66.700
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 22945.236 Da / Num. of mol.: 1 / Fragment: Residues 12-216
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: aidD, alkB, b2212, JW2200 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P05050, 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: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-MD6 / N-[(3-hydroxypyridin-2-yl)carbonyl]glycine


Type: peptide linking / Mass: 196.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8N2O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.13 Å3/Da / Density % sol: 42.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG 3350, 0.1M bis-tris pH6.5, 0.44mM ammonium iron(II) sulphate, 1mM 2-(3-hydroxypicolinomido)acetic acid, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5412 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 5, 2011 / Details: osmic HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5412 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 46973 / Num. obs: 12688 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 29.7 Å2 / Rmerge(I) obs: 0.043 / Χ2: 1.092 / Net I/σ(I): 28.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2-2.073.20.2184.30712601.31597.9
2.07-2.153.70.156.32112601.04698.5
2.15-2.253.70.1159.19512521.05299
2.25-2.373.70.110.71312631.07898.9
2.37-2.523.70.08513.29212821.1299.4
2.52-2.713.80.07215.24212771.06299.7
2.71-2.993.80.05619.61512781.009100
2.99-3.423.80.04325.6151269199.9
3.42-4.313.80.03435.81712781.187100
4.31-503.80.02936.22512691.09598.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å22.91 Å
Translation2.5 Å22.91 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.3.0phasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T4H

3t4h


Resolution: 2.001→22.913 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.84 / SU ML: 0.45 / Isotropic thermal model: Isotropic / σ(F): 1.98 / Phase error: 23.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2207 639 5.04 %random
Rwork0.1816 ---
obs0.1837 12687 99.13 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.206 Å2 / ksol: 0.376 e/Å3
Displacement parametersBiso max: 101.86 Å2 / Biso mean: 37.7623 Å2 / Biso min: 14.57 Å2
Baniso -1Baniso -2Baniso -3
1--2.7799 Å25.5295 Å20.304 Å2
2--0.1562 Å2-4.1363 Å2
3---2.6237 Å2
Refinement stepCycle: LAST / Resolution: 2.001→22.913 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1504 0 15 85 1604
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011588
X-RAY DIFFRACTIONf_angle_d1.2542174
X-RAY DIFFRACTIONf_chiral_restr0.068227
X-RAY DIFFRACTIONf_plane_restr0.004292
X-RAY DIFFRACTIONf_dihedral_angle_d14.684574
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.0013-2.15570.28951290.217923792508250898
2.1557-2.37240.23271210.189123932514251499
2.3724-2.71520.28471280.2046243325612561100
2.7152-3.41910.221310.1803242525562556100
3.4191-22.91430.18931300.1674241825482548100
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)
13.4774-1.15191.14043.40131.53551.5860.16030.1495-0.2193-0.0878-0.25610.34010.0935-0.1128-0.03830.2076-0.01780.06580.19890.02670.19910.5899-1.9663-6.1961
24.04313.2988-0.76692.7062-0.42662.9126-0.3988-0.8418-1.16180.68540.17480.45210.6502-0.64640.26690.52220.12310.21320.51330.18680.47723.5766-11.69975.6565
32.7374-1.1053-0.94072.5663-0.08251.8764-0.0658-0.28830.29480.05760.093-0.5051-0.00370.3039-0.02060.10270.0011-0.01080.1774-0.04240.3078.9112-1.8198-2.2628
43.9792-1.6225-1.11083.94770.25721.0816-0.146-0.34-0.2360.38090.21620.19370.02050.0937-0.06340.16620.0194-0.01330.190.01170.1112-4.45514.10070.9721
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 16:65)A0
2X-RAY DIFFRACTION2chain 'A' and (resseq 66:79)A0
3X-RAY DIFFRACTION3chain 'A' and (resseq 80:122)A0
4X-RAY DIFFRACTION4chain 'A' and (resseq 123:214)A0

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