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- PDB-3t4v: Crystal Structure of AlkB in complex with Fe(III) and N-Oxalyl-S-... -

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Basic information

Entry
Database: PDB / ID: 3t4v
TitleCrystal Structure of AlkB in complex with Fe(III) and N-Oxalyl-S-(2-napthalenemethyl)-L-cysteine
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 / oxidative demethylation / DNA alkylation repair / dioxygenase activity / ferrous iron binding ...response to methyl methanesulfonate / oxidative RNA demethylation / DNA oxidative demethylase / oxidative RNA demethylase activity / broad specificity oxidative DNA demethylase activity / RNA repair / oxidative demethylation / DNA alkylation repair / dioxygenase activity / ferrous iron binding / DNA repair / cytosol / 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
: / Chem-MD3 / Alpha-ketoglutarate-dependent dioxygenase AlkB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.732 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 26, 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)23,4274
Polymers22,9451
Non-polymers4813
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.070, 39.234, 40.261
Angle α, β, γ (deg.)76.330, 74.560, 65.280
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


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-MD3 / N-(carboxycarbonyl)-S-(naphthalen-2-ylmethyl)-L-cysteine


Type: L-peptide linking / Mass: 333.359 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15NO5S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.21 Å3/Da / Density % sol: 44.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% PEG 3350, 0.2M ammonium sulfate, 0.1M tris-hydrochloride pH8.5, 2.2mM ammonium iron(II) sulfate, 1mM N-Oxalyl-S-(2-napthalenemethyl)-L-cysteine, 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: Apr 11, 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: 1.7→50 Å / Num. all: 22000 / Num. obs: 20297 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 4.4 % / Biso Wilson estimate: 20.07 Å2 / Rmerge(I) obs: 0.107 / Χ2: 1.091 / Net I/σ(I): 23.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.7-1.761.90.2822.85217761.29981.2
1.76-1.832.40.2863.39319041.40787.8
1.83-1.913.10.2614.03320001.31792
1.91-2.0240.2384.87920921.24796.7
2.02-2.145.30.1866.58821701.08698.6
2.14-2.315.40.1467.92821191.00696.9
2.31-2.545.40.1199.82121201.03798.1
2.54-2.915.40.10110.90121361.06997.6
2.91-3.665.10.0919.95720181.02292.5
3.662-505.70.09710.41419620.98190.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å21.05 Å
Translation2.5 Å21.05 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: 1.732→22.994 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8641 / SU ML: 0.41 / Isotropic thermal model: Isotropic / σ(F): 1.97 / Phase error: 21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2019 1889 9.82 %random
Rwork0.1608 ---
obs0.1649 19227 94.06 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.788 Å2 / ksol: 0.397 e/Å3
Displacement parametersBiso max: 70.42 Å2 / Biso mean: 27.7213 Å2 / Biso min: 13.71 Å2
Baniso -1Baniso -2Baniso -3
1--1.8522 Å22.5271 Å2-2.4013 Å2
2---0.3767 Å2-5.2169 Å2
3---2.2289 Å2
Refinement stepCycle: LAST / Resolution: 1.732→22.994 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1544 0 30 213 1787
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111644
X-RAY DIFFRACTIONf_angle_d1.4862240
X-RAY DIFFRACTIONf_chiral_restr0.112234
X-RAY DIFFRACTIONf_plane_restr0.009294
X-RAY DIFFRACTIONf_dihedral_angle_d14.023600
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.7324-1.77920.26121410.209812011342134285
1.7792-1.83160.24251310.216612721403140389
1.8316-1.89060.26611260.201113031429142991
1.8906-1.95820.2511580.186413651523152396
1.9582-2.03650.20791450.178313851530153098
2.0365-2.12920.23551490.161713781527152799
2.1292-2.24130.2171600.150713841544154497
2.2413-2.38160.18391450.156513651510151097
2.3816-2.56530.20681490.15613931542154298
2.5653-2.8230.22311560.152613871543154398
2.823-3.23060.21031500.151613581508150896
3.2306-4.06650.18511360.144512401376137688
4.0665-22.99650.16541430.163913071450145092
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)
12.6615-0.0844-1.75144.49762.32774.1665-0.04760.16270.2339-0.3025-0.14690.1349-0.87760.05540.0460.1599-0.0043-0.02020.16340.02280.22981.871513.5894-3.5742
25.92082.3902-1.59225.4805-0.84313.07920.02880.0521-0.24830.0114-0.0382-0.07290.17190.10880.03380.11930.0209-0.07120.1001-0.0250.1048-1.0035-8.3605-6.7394
33.1157-0.89370.83956.6109-2.0187.8364-0.0522-0.4095-0.20130.40150.03980.0190.3041-0.41920.00120.1610.0011-0.00860.1666-0.03190.19392.4771-11.69233.7637
43.47373.6477-2.01554.9475-3.45353.1411-0.03720.0346-0.06610.1097-0.0112-0.01550.0177-0.06250.04820.16630.0230.01360.154-0.00650.27338.6535-13.585-3.424
51.0376-1.4362-1.46292.082.0782.0928-0.01990.07470.1939-0.18460.3317-0.6838-0.21640.3352-0.31090.19-0.00480.01570.23110.01880.271412.66536.486-4.1917
63.21632.44262.26966.18993.14672.92070.08210.0457-0.08430.23950.1445-0.46590.07940.219-0.26230.1690.01540.01480.16120.01010.18676.9071.42280.9144
76.05320.88432.69991.92990.67874.61740.2973-0.669-0.54950.39970.0707-0.14180.4503-0.0933-0.3660.20020.05160.00360.16940.01320.1731-1.9662-0.74647.3957
82.09650.03080.8941.41290.2481.2559-0.073-0.2226-0.01670.14280.05810.0921-0.0429-0.17130.01930.1530.01020.0130.16430.01630.1586-4.73285.3157-0.3144
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 15:29)A0
2X-RAY DIFFRACTION2chain 'A' and (resseq 30:59)A0
3X-RAY DIFFRACTION3chain 'A' and (resseq 60:79)A0
4X-RAY DIFFRACTION4chain 'A' and (resseq 80:93)A0
5X-RAY DIFFRACTION5chain 'A' and (resseq 94:106)A0
6X-RAY DIFFRACTION6chain 'A' and (resseq 107:122)A0
7X-RAY DIFFRACTION7chain 'A' and (resseq 123:142)A0
8X-RAY DIFFRACTION8chain 'A' and (resseq 143:214)A0

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