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- PDB-3khb: Crystal structure of Escherichia coli AlkB with Co(II) and 2-OG -

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Basic information

Entry
Database: PDB / ID: 3khb
TitleCrystal structure of Escherichia coli AlkB with Co(II) and 2-OG
ComponentsAlpha-ketoglutarate-dependent dioxygenase alkB
KeywordsOXIDOREDUCTASE / AlkB / 2-oxoglutarate / DNA alkylation repair / Dioxygenase / DNA damage / DNA repair / Iron / Metal-binding
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 / : / Alpha-ketoglutarate-dependent dioxygenase AlkB
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 1.2Sep 6, 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.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

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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: Alpha-ketoglutarate-dependent dioxygenase alkB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2026
Polymers48,7922
Non-polymers4104
Water54030
1
A: Alpha-ketoglutarate-dependent dioxygenase alkB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6013
Polymers24,3961
Non-polymers2052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alpha-ketoglutarate-dependent dioxygenase alkB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6013
Polymers24,3961
Non-polymers2052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)148.624, 42.806, 86.454
Angle α, β, γ (deg.)90.00, 121.77, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 24395.814 Da / Num. of mol.: 2
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
#2: Chemical ChemComp-CO / COBALT (II) ION


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


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


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.4 Å3/Da / Density % sol: 48.66 %
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.9→30.02 Å / Num. all: 10013 / Num. obs: 9374 / % possible obs: 93.61 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.21 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 6.8
Reflection shellResolution: 2.9→2.975 Å / Redundancy: 4.43 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 6.8 / Num. unique all: 594 / % possible all: 76.74

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0063refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FD8
Resolution: 2.9→30.02 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.83 / SU B: 52.338 / SU ML: 0.449 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.544 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30723 486 4.9 %RANDOM
Rwork0.23029 ---
obs0.23413 9374 93.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20.01 Å2
2---0.04 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3185 0 22 30 3237
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223297
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0621.9574489
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4685407
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.35723.117154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.97515492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2771526
X-RAY DIFFRACTIONr_chiral_restr0.0660.2471
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0222616
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_it0.2061.52044
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.38623278
X-RAY DIFFRACTIONr_scbond_it0.4531253
X-RAY DIFFRACTIONr_scangle_it0.7884.51211
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 33 -
Rwork0.353 561 -
obs--76.74 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.0323-0.34620.39416.9794-7.85648.8544-0.08990.0391-0.04620.0114-0.0353-0.1817-0.0317-0.01420.12520.4307-0.04770.13010.5325-0.11050.585934.6674.322412.0597
24.36950.3006-3.77517.32441.58163.74740.34460.87910.3331-0.0091-0.10830.5122-0.2351-0.8379-0.23630.2943-0.0568-0.18310.40080.0520.398436.78022.067716.209
37.3129-0.9061.96733.1053-1.11511.97690.1237-0.2222-0.86760.1759-0.05490.12760.4096-0.1035-0.06880.3637-0.04890.0060.25420.0030.174748.3832-9.124727.8134
40.27071.1712-0.40216.4719-1.82331.4287-0.00530.05470.1617-0.0980.16650.1519-0.16220.1337-0.16110.2977-0.0005-0.00430.31070.00680.330564.76215.274524.8506
52.3882-0.6350.17010.7957-1.4173.14740.14990.03090.0487-0.0329-0.1009-0.0099-0.21930.0349-0.0490.41470.07720.0520.38160.03360.194859.95411.472723.2947
62.46391.1127-0.00734.1931.18121.08940.0867-0.0630.18970.11340.018-0.2556-0.15350.148-0.10470.31270.0256-0.00940.33320.02550.313466.04432.234118.2726
71.1739-0.47080.49586.24320.62395.7060.05020.16320.2626-0.3391-0.1678-0.22010.20160.26690.11760.27350.01150.060.3181-0.0180.247266.1779-4.062318.5443
83.5185-0.1194-0.42011.60330.14430.0843-0.0101-0.1475-0.1395-0.0678-0.0350.08240.09250.00540.04510.4167-0.01080.01670.37630.0040.283358.5935-12.726121.4979
90.25520.00420.73972.7511-0.04715.35780.0382-0.1422-0.2091-0.0277-0.2079-0.06910.03190.12830.16970.4078-0.0231-0.00160.4520.05910.501644.558-11.091116.4459
1011.09086.78652.4164.55350.57222.5801-0.06310.0594-0.019-0.2706-0.1514-0.10080.4840.48360.21450.35390.0073-0.00940.3621-0.01640.291242.5162-6.34757.4153
112.55041.1053-1.05594.33031.69831.6488-0.15290.0393-0.33070.2307-0.14410.08880.2631-0.11180.2970.42310.0675-0.02220.3153-0.02260.335853.7037-5.686616.6106
122.2015-2.0533-0.31473.79461.65581.0354-0.11870.08130.0563-0.0211-0.01740.0962-0.10980.02660.1360.254-0.0404-0.0390.31480.010.318452.78878.857225.5974
131.411-1.6887-0.98046.09856.4817.59820.23590.04220.1209-0.07660.0708-0.29620.14160.1073-0.30670.3115-0.01910.02090.34110.01040.299357.17013.60638.2765
140.0467-0.21580.07871.125-0.18431.48790.0338-0.03110.0469-0.14950.0806-0.1444-0.2195-0.186-0.11440.30080.0166-0.00820.2056-0.01020.26147.28916.238515.2823
155.28713.67980.7843.77530.03090.3363-0.05310.04890.6238-0.0487-0.20710.0566-0.01680.13340.26020.4770.05370.06190.3075-0.00050.351943.470115.987715.2006
163.8338-2.10381.57282.4837-0.74510.6574-0.0006-0.0027-0.0501-0.0762-0.00470.0383-0.03570.00290.00530.3154-0.066-0.05150.2351-0.07060.287442.2632.795916.4124
175.953-1.3526-3.9380.32320.87232.63760.17940.5134-0.0092-0.0868-0.12350.0507-0.0392-0.3364-0.05590.4459-0.02210.03780.12940.00630.288150.05278.8417.9412
180.02910.043-0.34371.9584-1.78494.96440.01630.0168-0.00360.16460.11770.1795-0.2332-0.1981-0.1340.21260.0097-0.00510.2527-0.00490.237246.4779.927928.2559
191.38010.2515-1.71780.33640.78336.329-0.0072-0.1359-0.01430.02840.0111-0.02540.05090.2258-0.00390.30110.0129-0.00240.24310.00070.290446.2252-0.283830.5948
204.2897-3.51851.0338.78435.84087.84440.10580.13660.2963-0.61310.2089-0.5733-0.49790.386-0.31470.4715-0.0770.02350.2453-0.02670.301454.7039-5.24439.7637
211.90251.08010.43473.20424.80968.13470.06870.1240.17050.0376-0.01840.04540.0141-0.1327-0.05030.2702-0.04030.03080.3391-0.02660.3205-6.071-7.176252.7616
223.79750.1068-2.94620.0115-0.08112.3366-0.53450.4137-0.81030.0073-0.0896-0.06550.2354-0.4180.62410.6552-0.0136-0.0470.6280.050.5297-1.0726-7.278259.6219
233.9812-1.08994.96120.3-1.35946.1838-0.1790.05250.12830.03980.0169-0.0417-0.23090.04050.16210.3692-0.01180.1010.43390.03330.288-2.4606-2.175947.6253
246.00592.2024-1.06543.1946-0.24450.203-0.0254-0.1043-0.1622-0.1375-0.0035-0.1998-0.0178-0.01920.0290.41690.0037-0.01730.37190.02480.37471.62977.09143.3331
250.7579-2.64160.6789.5943-2.72870.95280.13720.02360.109-0.19330.0551-0.063-0.1653-0.1123-0.19230.49580.05170.0640.47460.10340.43611.946710.637144.0235
263.7302-4.3024-1.06445.40960.10613.1960.2373-0.01310.1314-0.2380.0218-0.0532-0.3313-0.091-0.2590.3646-0.0057-0.00610.389-0.00310.388321.36258.484548.09
270.2715-1.25660.54486.4725-2.8581.2693-0.1828-0.08570.01970.37190.2660.169-0.1198-0.0972-0.08320.43670.012-0.04510.4936-0.05570.345623.6517-0.169253.6211
283.6018-5.93260.39659.9685-0.08811.7096-0.01580.04690.24910.03550.0241-0.3783-0.01780.3074-0.00820.4039-0.03720.0190.3779-0.00590.412122.78334.225660.1298
296.5151.7120.70782.2195-0.81560.6746-0.3433-0.38780.486-0.1116-0.1509-0.68710.05320.08210.49420.51390.03460.01390.5218-0.1130.45825.58297.610859.3165
305.40633.19571.58072.96481.80761.46760.4001-0.02480.99240.0417-0.19240.3438-0.09930.006-0.20760.40870.02810.07630.3165-0.03410.58676.552110.785954.3568
315.4881-1.39872.50680.363-0.64351.1485-0.06440.14320.1650.0559-0.004-0.0347-0.06270.050.06840.37220.00650.04270.353-0.01320.3226-1.69633.571763.6556
321.4208-0.6733-0.80572.29583.31066.3926-0.08180.0396-0.07890.1203-0.06680.3230.16780.00680.14860.3394-0.00910.00690.29460.00120.331912.87993.837254.3236
330.23180.0383-1.00750.88930.35965.1445-0.02170.05350.03240.0950.016-0.10180.1038-0.12710.00570.2888-0.0024-0.0160.3389-0.03190.33616.8354-7.263357.171
341.4372-0.51030.73141.1821-0.70780.57430.00590.2750.2129-0.0324-0.0902-0.08620.03740.13580.08430.31020.00730.00350.37160.00380.24457.15120.661361.1586
354.60862.0338-1.64299.22722.34431.7181-0.67470.4567-0.74650.08870.220.20340.3961-0.1350.45470.38420.01970.03140.4334-0.03120.29418.8561-10.667148.7029
362.17370.68580.23654.0817-1.50071.92640.077-0.1075-0.40580.13240.4812-0.03380.427-0.2504-0.55810.3938-0.0106-0.00780.4024-0.10210.45417.805-14.205257.3559
371.7331-0.66043.61871.362-1.62627.6420.01630.12860.0543-0.0092-0.13890.03290.12070.33990.12270.2910.01280.02520.3191-0.00260.30443.1103-4.935159.9612
384.59970.2050.33950.0286-0.20432.6016-0.02410.2707-0.4862-0.00430.0316-0.03420.107-0.1082-0.00740.3724-0.03670.04960.2822-0.00220.31611.9587-10.198458.0908
398.158-3.62774.36576.9836-0.87293.686-0.0562-0.45430.1614-0.6131-0.2493-0.71930.1922-0.28310.30550.4544-0.04410.09510.53320.06310.300610.0868-3.521637.9253
401.1419-0.4919-1.87842.23771.21546.0990.0550.01180.0439-0.01730.1834-0.0422-0.02410.0841-0.23840.28740.0062-0.00180.31480.00710.342510.62273.946758.0921
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 17
2X-RAY DIFFRACTION2A18 - 24
3X-RAY DIFFRACTION3A25 - 46
4X-RAY DIFFRACTION4A47 - 52
5X-RAY DIFFRACTION5A53 - 66
6X-RAY DIFFRACTION6A67 - 74
7X-RAY DIFFRACTION7A75 - 85
8X-RAY DIFFRACTION8A86 - 95
9X-RAY DIFFRACTION9A96 - 102
10X-RAY DIFFRACTION10A103 - 112
11X-RAY DIFFRACTION11A113 - 120
12X-RAY DIFFRACTION12A121 - 131
13X-RAY DIFFRACTION13A132 - 138
14X-RAY DIFFRACTION14A139 - 161
15X-RAY DIFFRACTION15A162 - 169
16X-RAY DIFFRACTION16A170 - 181
17X-RAY DIFFRACTION17A182 - 186
18X-RAY DIFFRACTION18A187 - 196
19X-RAY DIFFRACTION19A197 - 208
20X-RAY DIFFRACTION20A209 - 214
21X-RAY DIFFRACTION21B9 - 15
22X-RAY DIFFRACTION22B16 - 22
23X-RAY DIFFRACTION23B23 - 27
24X-RAY DIFFRACTION24B28 - 33
25X-RAY DIFFRACTION25B34 - 42
26X-RAY DIFFRACTION26B43 - 47
27X-RAY DIFFRACTION27B48 - 66
28X-RAY DIFFRACTION28B67 - 72
29X-RAY DIFFRACTION29B73 - 87
30X-RAY DIFFRACTION30B88 - 103
31X-RAY DIFFRACTION31B104 - 112
32X-RAY DIFFRACTION32B113 - 122
33X-RAY DIFFRACTION33B123 - 136
34X-RAY DIFFRACTION34B137 - 149
35X-RAY DIFFRACTION35B150 - 155
36X-RAY DIFFRACTION36B156 - 172
37X-RAY DIFFRACTION37B173 - 182
38X-RAY DIFFRACTION38B183 - 192
39X-RAY DIFFRACTION39B193 - 204
40X-RAY DIFFRACTION40B205 - 214

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