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BMRB: 6685

NMR Structure of AlkB

Authors

Shivarattan, T., Matthews, S.

Assembly

AlkB

Entity

1. AlkB (polymer, Thiol state: not reported), 217 monomers, 24106.21 Da Detail

MALDLFADGE PWQEPLAAGA VILRRFAFNA AEQLIRDIND VASQSPFRQM VTPGGYTMSV AMTNCGHLGW TSHRQGYLYS PIDPQTNKPW PAMPQSFHNL CQRAATAAGY PDFQPDACLI NRYAPGAKLS LHQDKDEPDL RAPIVSVSLG LPAIFQFGGL KRNDPLKRLL LEHGDVVVWG GESRLFYHGI QPLKAGFHPL TTDCRYNLTF RQAGKKE

2. FE2 (non-polymer), 55.845 Da
3. 2-OXOGLUTARIC ACID (non-polymer), 146.098 Da

Total weight

24308.154 Da

Max. entity weight

24106.21 Da

Source organism

Escherichia coli

Exptl. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 90.3 %, Completeness: 61.0 %, Completeness (bb): 84.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	61.0 % (1540 of 2525)	52.8 % (694 of 1315)	68.0 % (670 of 986)	78.6 % (176 of 224)
Backbone	84.6 % (1071 of 1266)	79.3 % (344 of 434)	87.0 % (551 of 633)	88.4 % (176 of 199)
Sidechain	44.2 % (644 of 1458)	39.7 % (350 of 881)	53.3 % (294 of 552)	0.0 % (0 of 25)
Aromatic	0.0 % (0 of 242)	0.0 % (0 of 121)	0.0 % (0 of 117)	0.0 % (0 of 4)
Methyl	62.6 % (139 of 222)	61.3 % (68 of 111)	64.0 % (71 of 111)

1. AlkB

MALDLFADGE PWQEPLAAGA VILRRFAFNA AEQLIRDIND VASQSPFRQM VTPGGYTMSV AMTNCGHLGW TSHRQGYLYS PIDPQTNKPW PAMPQSFHNL CQRAATAAGY PDFQPDACLI NRYAPGAKLS LHQDKDEPDL RAPIVSVSLG LPAIFQFGGL KRNDPLKRLL LEHGDVVVWG GESRLFYHGI QPLKAGFHPL TTDCRYNLTF RQAGKKE

Show sample condition

Sample

Temperature 310 (±1) K, pH 7.6 (±0.1), Details AlkB + co-factors in Tris-HCl Buffer

#	Name	Isotope labeling	Type	Concentration
1	AlkB		protein	0.30 mM
2	Ferrous Sulphate		ligand	5 (±0.5) mM
3	2-oxoglutarate		ligand	10 (±0.5) mM
4	Ascorbic acid		reducing agent	20 (±0.5) mM
5	Sodium Dithionite		reducing agent	2 (±1.0) mM
6	Tris-HCl		buffer	50 (±0.5) mM

Release date

2005-06-12

Citation

Resonance assignments of Escherichia coli AlkB: a key 2-oxoglutarate and Fe(II) dependent dioxygenase of the adaptive DNA-repair response
Shivarattan, T., Chen, H., Simpson, P., Sedgwick, B., Matthews, S.
J. Biomol. NMR (2005), 33, 138-138, PubMed 16258838 , DOI 10.1007/s10858-005-3040-1 , Abstract

Related entities 1. AlkB, : 45 entities Detail

Interaction partners 1. AlkB, : 4 interactors Detail

More details for 4 interactors identified by 3 citations

Experiments performed 6 experiments Detail

1 1H15N_HSQC

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Temperature 310 (±1) K, pH 7.6 (±0.1), Details AlkB + co-factors in Tris-HCl Buffer

#	Name	Isotope labeling	Type	Concentration
1	AlkB		protein	0.30 mM
2	Ferrous Sulphate		ligand	5 (±0.5) mM
3	2-oxoglutarate		ligand	10 (±0.5) mM
4	Ascorbic acid		reducing agent	20 (±0.5) mM
5	Sodium Dithionite		reducing agent	2 (±1.0) mM
6	Tris-HCl		buffer	50 (±0.5) mM

2 HNCACB(CO)NH

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Temperature 310 (±1) K, pH 7.6 (±0.1), Details AlkB + co-factors in Tris-HCl Buffer

#	Name	Isotope labeling	Type	Concentration
1	AlkB		protein	0.30 mM
2	Ferrous Sulphate		ligand	5 (±0.5) mM
3	2-oxoglutarate		ligand	10 (±0.5) mM
4	Ascorbic acid		reducing agent	20 (±0.5) mM
5	Sodium Dithionite		reducing agent	2 (±1.0) mM
6	Tris-HCl		buffer	50 (±0.5) mM

3 CBCA(CO)NH

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Temperature 310 (±1) K, pH 7.6 (±0.1), Details AlkB + co-factors in Tris-HCl Buffer

#	Name	Isotope labeling	Type	Concentration
1	AlkB		protein	0.30 mM
2	Ferrous Sulphate		ligand	5 (±0.5) mM
3	2-oxoglutarate		ligand	10 (±0.5) mM
4	Ascorbic acid		reducing agent	20 (±0.5) mM
5	Sodium Dithionite		reducing agent	2 (±1.0) mM
6	Tris-HCl		buffer	50 (±0.5) mM

4 HNCO

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Temperature 310 (±1) K, pH 7.6 (±0.1), Details AlkB + co-factors in Tris-HCl Buffer

#	Name	Isotope labeling	Type	Concentration
1	AlkB		protein	0.30 mM
2	Ferrous Sulphate		ligand	5 (±0.5) mM
3	2-oxoglutarate		ligand	10 (±0.5) mM
4	Ascorbic acid		reducing agent	20 (±0.5) mM
5	Sodium Dithionite		reducing agent	2 (±1.0) mM
6	Tris-HCl		buffer	50 (±0.5) mM

5 HN(CA)CO

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Temperature 310 (±1) K, pH 7.6 (±0.1), Details AlkB + co-factors in Tris-HCl Buffer

#	Name	Isotope labeling	Type	Concentration
1	AlkB		protein	0.30 mM
2	Ferrous Sulphate		ligand	5 (±0.5) mM
3	2-oxoglutarate		ligand	10 (±0.5) mM
4	Ascorbic acid		reducing agent	20 (±0.5) mM
5	Sodium Dithionite		reducing agent	2 (±1.0) mM
6	Tris-HCl		buffer	50 (±0.5) mM

6 HCCH_TOCSY

Instrument

Bruker DRX - 500 MHz

Sample

State isotropic, Temperature 310 (±1) K, pH 7.6 (±0.1), Details AlkB + co-factors in Tris-HCl Buffer

#	Name	Isotope labeling	Type	Concentration
1	AlkB		protein	0.30 mM
2	Ferrous Sulphate		ligand	5 (±0.5) mM
3	2-oxoglutarate		ligand	10 (±0.5) mM
4	Ascorbic acid		reducing agent	20 (±0.5) mM
5	Sodium Dithionite		reducing agent	2 (±1.0) mM
6	Tris-HCl		buffer	50 (±0.5) mM

Chemical shift validation 5 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr6685_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Content subtype: bmr6685_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	chem_shift_list_1	Warning	1520		86.2 (chain: 1, length: 217)
1	Chemical shift references	chemical_shift_referencing	OK	3		No information

Assigned chemical shifts

Saveframe: chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 217, Sequence coverage: 86.2%
- Total number of assignments
  - ¹H chemical shifts: 735
  - ¹³C chemical shifts: 618
  - ¹⁵N chemical shifts: 167
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1