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- PDB-3khc: Crystal Structure of Escherichia coli AlkB in complex with ssDNA ... -

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Basic information

Entry
Database: PDB / ID: 3khc
TitleCrystal Structure of Escherichia coli AlkB in complex with ssDNA containing a 1-methylguanine lesion
Components
  • Alpha-ketoglutarate-dependent dioxygenase alkB
  • DNA (5'-D(P*GP*CP*AP*T)-3')
  • DNA (5'-D(P*TP*AP*(MG1)P*TP*GP*CP*CP*T)-3')
Keywordsoxidoreductase/DNA / oxidoreductase / 1-methylguanine / AlkB / 2-oxoglutarate / Dioxygenase / DNA damage / DNA repair / Iron / Metal-binding / oxidoreductase-DNA 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
2-OXOGLUTARIC ACID / : / DNA / Alpha-ketoglutarate-dependent dioxygenase AlkB
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHollis, T. / Holland, P.J.
CitationJournal: Plos One / Year: 2010
Title: Structural and mutational analysis of Escherichia coli AlkB provides insight into substrate specificity and DNA damage searching.
Authors: Holland, P.J. / Hollis, T.
History
DepositionOct 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / 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.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.value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-ketoglutarate-dependent dioxygenase alkB
B: Alpha-ketoglutarate-dependent dioxygenase alkB
C: DNA (5'-D(P*TP*AP*(MG1)P*TP*GP*CP*CP*T)-3')
D: DNA (5'-D(P*GP*CP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7368
Polymers52,3264
Non-polymers4104
Water4,846269
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)147.809, 41.441, 85.622
Angle α, β, γ (deg.)90.00, 120.98, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-335-

HOH

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 24351.805 Da / Num. of mol.: 2 / Mutation: D135A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: aidD, alkB, b2212, JW2200 / Plasmid: pET-19b / Production host: Escherichia coli (E. coli) / Strain (production host): C41(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

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain DNA (5'-D(P*TP*AP*(MG1)P*TP*GP*CP*CP*T)-3')


Mass: 2431.630 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(P*GP*CP*AP*T)-3')


Mass: 1190.830 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 3 types, 273 molecules

#4: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#5: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 2.15 Å3/Da / Density % sol: 42.75 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 10-20% PEG 8000, 0.1M MES, 0.1M sodium chloride, 0.1M magnesium chloride, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 288K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2MES11
3sodium chloride11
4magnesium chloride11
5PEG 800012
6MES12
7sodium chloride12
8magnesium chloride12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: May 12, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→42.69 Å / Num. all: 22909 / Num. obs: 21726 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.94 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 9.4
Reflection shellResolution: 2.2→2.23 Å / Redundancy: 6.27 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 9.4 / Num. unique all: 1661 / % possible all: 99.94

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0063refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FD8

2fd8


Resolution: 2.2→23.74 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.9 / SU B: 15.38 / SU ML: 0.191 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.372 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27326 1156 5.1 %RANDOM
Rwork0.21126 ---
obs0.21434 21726 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.165 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20.15 Å2
2---0.13 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 2.2→23.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3243 246 22 269 3780
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223712
X-RAY DIFFRACTIONr_angle_refined_deg1.6192.0485112
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6325431
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.97522.956159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.87915535
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6821528
X-RAY DIFFRACTIONr_chiral_restr0.0870.2543
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212834
X-RAY DIFFRACTIONr_mcbond_it0.3961.52099
X-RAY DIFFRACTIONr_mcangle_it0.73423385
X-RAY DIFFRACTIONr_scbond_it1.19131613
X-RAY DIFFRACTIONr_scangle_it1.9984.51717
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 74 -
Rwork0.241 1587 -
obs--99.94 %
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)
110.682-1.1389-4.82271.4566-1.7076.16690.04970.1327-0.23010.05940.33280.43760.0273-0.8567-0.38240.3343-0.05720.03580.3221-0.04070.3072-40.25718.68214.501
23.13240.5741-0.98792.8026-2.15524.15760.1604-0.0062-0.1649-0.25050.24780.60280.3536-0.7088-0.40820.2489-0.0504-0.03490.36440.00520.1795-36.57714.34617.603
39.5131-1.46561.42395.38960.61781.1230.1438-0.5547-0.9260.23740.02140.23660.6101-0.0999-0.16520.4015-0.0253-0.03670.14810.03460.097-22.642428.728
42.87640.3122-0.01378.6712-1.16892.14130.0846-0.18530.376-0.354-0.1445-0.4078-0.41440.43630.05990.2727-0.01710.04060.198-0.01210.0907-9.77619.55625.165
53.57980.6021.94487.20025.36725.953-0.09920.07480.2062-0.55310.1115-0.3067-0.37890.4461-0.01230.2150.00250.03940.19910.02740.0472-14.02316.25923.289
65.19592.77752.43591.83892.12933.11540.0573-0.08310.23310.073-0.00730.0140.1071-0.0183-0.05010.31510.10520.01110.1911-0.04240.263-11.62113.88517.311
79.3907-1.2717-2.96747.3961-0.75854.67260.47950.33240.95320.2552-0.2939-0.6966-0.38140.5595-0.18560.23450.00140.09530.2568-0.00570.2145-6.49218.09116.412
84.3903-0.2546-1.35940.88370.171911.2251-0.0173-0.0324-0.1502-0.0481-0.0252-0.1171-0.1785-0.0410.04250.16330.03420.0090.124-0.01020.1495-6.5757.39121.287
97.992.3264-2.40460.7587-0.47392.85380.28240.1116-0.52080.25210.0083-0.1480.63630.0576-0.29070.43110.0369-0.09070.1344-0.05740.3289-12.292.75721.159
105.871-0.22041.91440.1321-1.07628.8489-0.04270.2429-0.7246-0.10730.08860.00030.8103-0.6372-0.04590.3381-0.0671-0.01810.1412-0.0920.191-28.7322.67417.007
117.77750.2122-0.99291.085-2.37055.21550.11950.3979-0.4226-0.23310.11670.11860.4962-0.2839-0.23610.2711-0.0218-0.05470.3203-0.11140.0775-31.5988.6867.697
122.2923-0.55460.99510.3705-0.2872.4348-0.0166-0.0306-0.11840.14310.1285-0.04570.32920.1557-0.11190.26870.03750.01360.2003-0.03360.1024-20.81914.98722.878
130.5606-0.40350.64331.47840.27422.21960.01660.10350.0444-0.1092-0.0304-0.0787-0.0952-0.0260.01380.17440.01140.01950.2066-0.01070.0233-23.49818.6514.926
145.8882-2.0073-5.52723.30590.04038.21880.0646-0.00450.1556-0.3806-0.22830.1202-0.3226-0.02830.16370.32780.0395-0.07910.2285-0.05990.169-26.1128.68810.653
150.4457-1.89351.06758.1849-4.82468.70130.0278-0.06340.05780.05920.3468-0.0299-0.9416-0.6864-0.37460.41860.10950.10650.26630.00150.4078-29.01530.99315.096
162.43381.8397-2.46352.5095-1.17358.02740.08480.2379-0.2981-0.0931-0.09950.0245-0.1853-0.43340.01470.22640.0374-0.01080.2426-0.0570.1441-31.6417.37516.329
172.6654-2.086-1.16211.66320.83470.69090.18420.2831-0.0461-0.1236-0.28480.006-0.11690.04840.10060.24520.00860.02270.29910.03670.0859-24.05823.81911.248
188.6483.6303-1.836.3937-0.36591.75620.2431-0.2150.09390.2213-0.16680.5528-0.0458-0.2313-0.07630.22790.00660.00030.2148-0.01590.0674-29.85319.42933.292
192.32660.0297-0.58142.16950.85756.13510.05080.0078-0.0915-0.14250.0587-0.1059-0.13880.5563-0.10950.1731-0.01220.02560.15940.03140.0692-24.48714.05725.324
206.24293.5620.61418.6341.48860.6498-0.29420.4213-0.7728-0.18550.0765-0.11990.25250.18680.21770.46620.1540.08810.3154-0.0220.3137-17.3786.1984.74
214.30470.76343.99431.23861.75689.344-0.1697-0.12260.29610.0714-0.05270.032-0.2249-0.6050.22240.1871-0.05350.07450.2123-0.030.0679-34.057.741-18.286
226.2586-3.05580.33882.978-0.64820.17540.15630.0154-0.61720.07360.00350.6345-0.04250-0.15980.3195-0.04260.02820.2824-0.03970.1426-30.8618.823-18.107
231.5159-1.022-0.71041.12721.87644.83550.160.64310.3277-0.308-0.3575-0.0941-0.6276-0.04690.19750.3085-0.0422-0.03120.57140.13620.1791-27.2620.638-28.684
243.1661-1.6693-3.85080.90292.34079.56070.0229-0.02920.4636-0.07450.0101-0.2165-0.5471-0.2215-0.03290.3207-0.10020.01350.22120.11240.3578-12.43326.866-27.256
255.6054-0.51580.08524.8722-2.41371.2034-0.16110.68120.4021-0.0764-0.1688-0.68740.06210.03830.32980.2978-0.10650.06730.305-0.01950.1764-4.8217.05-23.547
266.19320.7181-0.4620.8865-0.09761.3240.03170.12780.07640.0702-0.0365-0.1045-0.20210.06750.00480.222-0.11230.05630.1957-0.0240.0403-6.84615.944-18.668
2725.696-3.994610.07560.6235-1.56563.9527-0.2356-0.2230.54550.04720.0248-0.0669-0.0707-0.09090.21080.2236-0.04570.01750.24-0.04890.1574-0.83816.998-12.018
287.2752-2.1097-1.96615.94694.48013.39740.1789-0.13130.56420.32610.2599-0.56520.22260.1898-0.43880.2342-0.09110.03030.1683-0.08310.1159-5.45522.089-13.88
290.25561.5042-0.00368.89430.16185.51070.04950.0020.00110.06750.041-0.0142-0.26140.1596-0.09040.2728-0.09230.0720.14220.0140.2479-10.14529.37-19.176
3010.08457.1968-5.90035.1443-4.21083.45970.24660.37660.73610.22850.18830.5241-0.2168-0.2403-0.43490.5876-0.0304-0.05980.3871-0.0260.3337-27.35124.904-19.013
316.3481.0868-2.61453.20050.68533.7636-0.0049-0.07990.73060.20280.13730.2505-0.1168-0.2002-0.13240.1756-0.03030.01210.1744-0.02540.0973-25.34720.185-12.104
324.75530.2057-2.23060.08780.32323.4969-0.12020.5486-0.4322-0.02770.075-0.06420.0647-0.2480.04530.2253-0.12510.07910.3638-0.16180.0953-11.7278.362-24.924
330.8289-0.2535-1.49053.64823.9776.15390.0885-0.149-0.09340.12510.331-0.5808-0.00370.5337-0.41950.29180.0624-0.04080.2234-0.10980.1779-15.89713.211-6.099
343.2689-0.42390.26190.94011.23494.2959-0.08160.3495-0.24950.05320.21550.00970.18730.1608-0.13390.1961-0.05650.05950.2319-0.08550.0658-21.5078.435-19.072
355.299-1.459.52388.3863-2.557517.13440.0634-0.2594-0.03780.2079-0.0312-0.18310.1852-0.436-0.03220.41280.01980.05790.2455-0.04270.3479-15.998-3.645-8.766
363.9523-0.15120.50799.6622-5.59947.22230.06720.6118-0.9486-0.20270.22330.50090.3734-0.3251-0.29050.1952-0.10860.01260.2813-0.1620.2585-24.2313.026-23.068
374.084-1.80544.39892.5860.63478.6525-0.0656-0.3885-0.0680.32150.15310.05430.4887-0.613-0.08750.2791-0.08780.03790.3336-0.01690.0848-25.91110.288-14.254
382.67320.54510.39790.4325-0.54442.2113-0.06050.295-0.47780.04270.0813-0.17160.36320.1327-0.02080.3394-0.00170.01470.1923-0.1220.1602-17.264.833-16.732
392.3924-0.8725-1.80557.6952.40221.79020.2490.8407-0.0111-0.4908-0.0719-0.8503-0.3108-0.4824-0.1770.3647-0.18280.06470.9467-0.00530.1036-19.13513.178-34.932
402.4769-0.1502-1.62990.6182-2.1259.197-0.22410.01890.34830.1064-0.0203-0.1466-0.19450.03090.24440.2439-0.03130.0280.1449-0.06210.1511-18.53420.118-11.575
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 15
2X-RAY DIFFRACTION2A16 - 28
3X-RAY DIFFRACTION3A29 - 45
4X-RAY DIFFRACTION4A46 - 54
5X-RAY DIFFRACTION5A55 - 66
6X-RAY DIFFRACTION6A67 - 71
7X-RAY DIFFRACTION7A72 - 78
8X-RAY DIFFRACTION8A79 - 85
9X-RAY DIFFRACTION9A86 - 93
10X-RAY DIFFRACTION10A94 - 102
11X-RAY DIFFRACTION11A103 - 112
12X-RAY DIFFRACTION12A113 - 127
13X-RAY DIFFRACTION13A128 - 154
14X-RAY DIFFRACTION14A155 - 160
15X-RAY DIFFRACTION15A161 - 169
16X-RAY DIFFRACTION16A170 - 181
17X-RAY DIFFRACTION17A182 - 189
18X-RAY DIFFRACTION18A190 - 200
19X-RAY DIFFRACTION19A201 - 210
20X-RAY DIFFRACTION20A211 - 216
21X-RAY DIFFRACTION21B9 - 18
22X-RAY DIFFRACTION22B19 - 23
23X-RAY DIFFRACTION23B24 - 36
24X-RAY DIFFRACTION24B37 - 45
25X-RAY DIFFRACTION25B46 - 50
26X-RAY DIFFRACTION26B51 - 68
27X-RAY DIFFRACTION27B69 - 74
28X-RAY DIFFRACTION28B75 - 84
29X-RAY DIFFRACTION29B85 - 93
30X-RAY DIFFRACTION30B94 - 102
31X-RAY DIFFRACTION31B103 - 119
32X-RAY DIFFRACTION32B120 - 130
33X-RAY DIFFRACTION33B131 - 140
34X-RAY DIFFRACTION34B141 - 159
35X-RAY DIFFRACTION35B160 - 164
36X-RAY DIFFRACTION36B165 - 172
37X-RAY DIFFRACTION37B173 - 181
38X-RAY DIFFRACTION38B182 - 193
39X-RAY DIFFRACTION39B194 - 205
40X-RAY DIFFRACTION40B206 - 215

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