BMRB Entry 6605

Name: E. Coli Ada in a complex with DNA
Published: 2005-10-28

Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR6605

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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:

E. Coli Ada in a complex with DNA

Deposition date:

2005-04-22

Original release date:

2005-10-28

Authors:

He, Chuan; Hus, Jean-Christophe; Sun, Li Jing; Zhou, Pei; Norman, Derek; Doetsch, Volker; Gross, John; Lane, William; Wagner, Gerhard; Verdine, Gregory

Citation:

Citation: He, Chuan; Hus, Jean-Christophe; Sun, Li Jing; Zhou, Pei; Norman, Derek; Dotsch, Volker; Wei, Hua; Gross, John; Lane, William; Wagner, Gerhard; Verdine, Gregory. "A Methylation-Dependent Electrostatic Switch Controls DNA Repair and Transcriptional Activation by E. coli Ada" Mol Cell 20, 117-129 (2005).
PubMed: 16209950

Assembly members:

Assembly members:
Ada, polymer, 139 residues, Formula weight is not available
Ada, polymer, 18 residues, Formula weight is not available
Ada, polymer, 18 residues, Formula weight is not available
ZN, non-polymer, 65.409 Da.

Natural source:

Natural source: Common Name: E. coli Taxonomy ID: 562 Superkingdom: Bacteria Kingdom: not available Genus/species: Escherichia coli

Experimental source:

Experimental source: Production method: recombinant technology Vector: pET-30a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Ada: MKKATCLTDDQRWQSVLARD PNADGEFVFAVRTTGIFXRP SCRARHALRENVSFYANASE ALAAGFRPCKRCQPDKANPR QHRLDKITHACRLLEQETPV TLEALADQVAMSPFHLHRLF KATTGMTPKAWQQAWRARR
Ada: TCTTGCGCTTTAATTTGC
Ada: GCAAATTAAAGCGCAAGA

Data sets:

assigned_chemical_shifts
- chem_shift_list_1

Data type	Count
13C chemical shifts	438
15N chemical shifts	142
1H chemical shifts	671

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Ada	1
2	Ada	2
3	Ada	3
4	Ada	4

Entities:

Entity 1, Ada 139 residues - Formula weight is not available

1

MET

LYS

ALA

THR

CYS

LEU

THR

ASP

2

GLN

ARG

TRP

GLN

SER

VAL

LEU

ALA

ARG

ASP

3

PRO

ASN

ALA

ASP

GLY

GLU

PHE

VAL

PHE

ALA

4

VAL

ARG

THR

GLY

ILE

PHE

SMC

ARG

PRO

5

SER

CYS

ARG

ALA

ARG

HIS

ALA

LEU

ARG

GLU

6

ASN

VAL

SER

PHE

TYR

ALA

ASN

ALA

SER

GLU

7

ALA

LEU

ALA

GLY

PHE

ARG

PRO

CYS

LYS

8

ARG

CYS

GLN

PRO

ASP

LYS

ALA

ASN

PRO

ARG

9

GLN

HIS

ARG

LEU

ASP

LYS

ILE

THR

HIS

ALA

10

CYS

ARG

LEU

GLU

GLN

GLU

THR

PRO

VAL

11

THR

LEU

GLU

ALA

LEU

ALA

ASP

GLN

VAL

ALA

12

MET

SER

PRO

PHE

HIS

LEU

HIS

ARG

LEU

PHE

13

LYS

ALA

THR

GLY

MET

THR

PRO

LYS

ALA

14

TRP

GLN

ALA

TRP

ARG

ALA

ARG

Entity 2, Ada 18 residues - Formula weight is not available

1

DT

DC

DT

DG

DC

DG

DC

DT

2

DT

DA

DT

DG

DC

Entity 3, Ada 18 residues - Formula weight is not available

1

DG

DC

DA

DT

DA

2

DG

DC

DG

DC

DA

DG

DA

Entity 4, Ada - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: Ada, {U-13C; U-15N; U-70% 2H], 0.5 mM; Ada 0.5 mM; Ada 0.5 mM; sodium phosphate 25 mM; NaCl 50 mM; DTT 5 mM

conditions_1: pH: 6.5; pressure: 1 atm; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
1H15N_HSQC	sample_1	not available	conditions_1
1H13C_HSQC 10% 13C	sample_1	not available	conditions_1
3D TROSY-HNCA 2H, 13C, 15N	sample_1	not available	conditions_1
3D TROSY-HN(CO)CA 2H, 13C, 15N	sample_1	not available	conditions_1
3D TROSY-HN(CA)CB 2H, 13C, 15N	sample_1	not available	conditions_1
3D TROSY-HN(COCA)CB 2H, 13C, 15N	sample_1	not available	conditions_1
3D TROSY-HN(CA)CO 2H, 13C, 15N	sample_1	not available	conditions_1
3D TROSY-HNCO 2H, 13C, 15N	sample_1	not available	conditions_1
3D H(CC-CO)NH-TOCSY 70% 2H, 15N, 13C	sample_1	not available	conditions_1
3D (H)C(C-CO)NH-TOCSY 70% 2H, 15N, 13C	sample_1	not available	conditions_1
3D HCCH-TOCSY 13C 13C	sample_1	not available	conditions_1
3D 15N-NOESY-HSQC mix=60ms 15N	sample_1	not available	conditions_1
3D 13C-NOESY-HSQC mix=100ms 13C	sample_1	not available	conditions_1
3D 13C-NOESY-HSQC mix=200ms 2H; 13C Methyl group of V,I,L; 1H of F,Y	sample_1	not available	conditions_1
2D NOESY mix=100ms D2O unlabeled DNA, 2H, 15N protein with only I delta1, L delta1,2 and V gamma1,2 13C	sample_1	not available	conditions_1
3D 15N-NOESY-HSQC mix=200ms 2H, 15N protein sample	sample_1	not available	conditions_1
3D 13C-NOESY-HSQC mix=100ms D2O 13C C5A labeled Thymine Top or Bottom Strand	sample_1	not available	conditions_1
3D 13C-NOESY-HSQC mix=100ms in H2O 13C Methyl group of Cys38	sample_1	not available	conditions_1

Software:

DYANA v1.5 -

X-PLOR v3.815 -

NMRPipe v2001 -

NMR spectrometers:

Varian INOVA 900 MHz
Varian INOVA 750 MHz
Varian INOVA 500 MHz
Bruker AVANCE 500 MHz

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