BMRB Entry 6685

Name: NMR Structure of AlkB
Published: 2005-11-07

Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR6685

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR Structure of AlkB

Deposition date:

2005-06-13

Original release date:

2005-11-07

Authors:

Shivarattan, Tara; Matthews, Stephen

Citation:

Citation: Shivarattan, Tara; Chen, Ho Ann; Simpson, Pete; Sedgwick, Barbara; Matthews, Stephen. "Resonance Assignments of Escherichia Coli AlkB: A Key 2-oxoglutarate and Fe(II) Dependent Dioxygenase of the Adaptive DNA-repair Response" J. Biomol. NMR 33, 138-138 (2005).
PubMed: 16258838

Assembly members:

Assembly members:
AlkB, polymer, 217 residues, Formula weight is not available
FE2, non-polymer, 55.845 Da.
2-OXOGLUTARIC ACID, non-polymer, 146.098 Da.

Natural source:

Natural source: Common Name: E. coli Taxonomy ID: 562 Superkingdom: Eubacteria Kingdom: Not applicable Genus/species: Escherichia Escherichia coli

Experimental source:

Experimental source: Production method: recombinant technology

Entity Sequences (FASTA):

Entity Sequences (FASTA):
AlkB: MALDLFADGEPWQEPLAAGA VILRRFAFNAAEQLIRDIND VASQSPFRQMVTPGGYTMSV AMTNCGHLGWTSHRQGYLYS PIDPQTNKPWPAMPQSFHNL CQRAATAAGYPDFQPDACLI NRYAPGAKLSLHQDKDEPDL RAPIVSVSLGLPAIFQFGGL KRNDPLKRLLLEHGDVVVWG GESRLFYHGIQPLKAGFHPL TTDCRYNLTFRQAGKKE

Data sets:

assigned_chemical_shifts
- chem_shift_list_1

Data type	Count
13C chemical shifts	618
15N chemical shifts	167
1H chemical shifts	735

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	AlkB	1
2	IRON (II) ION	2
3	2-oxoglutarate	3

Entities:

Entity 1, AlkB 217 residues - Formula weight is not available

1

MET

ALA

LEU

ASP

LEU

PHE

ALA

ASP

GLY

GLU

2

PRO

TRP

GLN

GLU

PRO

LEU

ALA

GLY

ALA

3

VAL

ILE

LEU

ARG

PHE

ALA

PHE

ASN

ALA

4

ALA

GLU

GLN

LEU

ILE

ARG

ASP

ILE

ASN

ASP

5

VAL

ALA

SER

GLN

SER

PRO

PHE

ARG

GLN

MET

6

VAL

THR

PRO

GLY

TYR

THR

MET

SER

VAL

7

ALA

MET

THR

ASN

CYS

GLY

HIS

LEU

GLY

TRP

8

THR

SER

HIS

ARG

GLN

GLY

TYR

LEU

TYR

SER

9

PRO

ILE

ASP

PRO

GLN

THR

ASN

LYS

PRO

TRP

10

PRO

ALA

MET

PRO

GLN

SER

PHE

HIS

ASN

LEU

11

CYS

GLN

ARG

ALA

THR

ALA

GLY

TYR

12

PRO

ASP

PHE

GLN

PRO

ASP

ALA

CYS

LEU

ILE

13

ASN

ARG

TYR

ALA

PRO

GLY

ALA

LYS

LEU

SER

14

LEU

HIS

GLN

ASP

LYS

ASP

GLU

PRO

ASP

LEU

15

ARG

ALA

PRO

ILE

VAL

SER

VAL

SER

LEU

GLY

16

LEU

PRO

ALA

ILE

PHE

GLN

PHE

GLY

LEU

17

LYS

ARG

ASN

ASP

PRO

LEU

LYS

ARG

LEU

18

LEU

GLU

HIS

GLY

ASP

VAL

TRP

GLY

19

GLY

GLU

SER

ARG

LEU

PHE

TYR

HIS

GLY

ILE

20

GLN

PRO

LEU

LYS

ALA

GLY

PHE

HIS

PRO

LEU

21

THR

ASP

CYS

ARG

TYR

ASN

LEU

THR

PHE

22

ARG

GLN

ALA

GLY

LYS

GLU

Entity 2, IRON (II) ION - Fe - 55.845 Da.

1

FE2

Entity 3, 2-oxoglutarate - C5 H6 O5 - 146.098 Da.

1

AKG

Samples:

sample_1: AlkB 0.30 mM; Ferrous Sulphate 5 ± 0.5 mM; 2-oxoglutarate 10 ± 0.5 mM; Ascorbic acid 20 ± 0.5 mM; Sodium Dithionite 2 ± 1 mM; Tris-HCl 50 ± 0.5 mM

conditions_1: pH: 7.6; temperature: 310 K

Experiments:

Name	Sample	Sample state	Sample conditions
1H15N_HSQC	sample_1	not available	conditions_1
HNCACB(CO)NH	sample_1	not available	conditions_1
CBCA(CO)NH	sample_1	not available	conditions_1
HNCO	sample_1	not available	conditions_1
HN(CA)CO	sample_1	not available	conditions_1
HCCH_TOCSY	sample_1	not available	conditions_1

Software:

NMRView v5.0 -

NMR spectrometers:

Bruker DRX 500 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks