BMRB Entry 7097

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PDB ID: 2glo
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR7097
MolProbity Validation Chart

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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:

DNA recognition by the Brinker nuclear repressor - an extreme case of the coupling between binding and folding

Deposition date:

2006-05-05

Original release date:

2006-09-22

Authors:

Cordier, F.; Hartmann, B.; Rogowski, M.; Affolter, M.; Grzesiek, S.

Citation:

Citation: Cordier, F.; Hartmann, B.; Rogowski, M.; Affolter, M.; Grzesiek, S.. "DNA recognition by the Brinker repressor - an extreme case of coupling between binding and folding" J. Mol. Biol. 361, 659-672 (2006).
PubMed: 16876822

Assembly members:

Assembly members:
brinker CG9653-PA, polymer, 59 residues, Formula weight is not available
5'-D(*TP*GP*AP*GP*GP*CP*GP*TP*CP*AP*AP*C)-3', polymer, 12 residues, Formula weight is not available
5'-D(*GP*TP*TP*GP*AP*CP*GP*CP*CP*TP*CP*A)-3', polymer, 12 residues, Formula weight is not available

Natural source:

Natural source: Common Name: Fruit fly Taxonomy ID: 7227 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Drosophila melanogaster

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET-22b(+)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
brinker CG9653-PA: GSRRIFTPHFKLQVLESYRN DNDCKGNQRATARKYNIHRR QIQKWLQCESNLRSSVANN
5'-D(*TP*GP*AP*GP*GP*CP*GP*TP*CP*AP*AP*C)-3': TGAGGCGTCAAC
5'-D(*GP*TP*TP*GP*AP*CP*GP*CP*CP*TP*CP*A)-3': GTTGACGCCTCA

Data sets:

assigned_chemical_shifts

Data type	Count
13C chemical shifts	255
15N chemical shifts	75
1H chemical shifts	582

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	brinker CG9653-PA	1
2	5'-D(TPGPAPGPGPCPGPTPCPAPAPC)-3'	2
3	5'-D(GPTPTPGPAPCPGPCPCPTPCPA)-3'	3

Entities:

Entity 1, brinker CG9653-PA 59 residues - Formula weight is not available

1

GLY

SER

ARG

ILE

PHE

THR

PRO

HIS

PHE

2

LYS

LEU

GLN

VAL

LEU

GLU

SER

TYR

ARG

ASN

3

ASP

ASN

ASP

CYS

LYS

GLY

ASN

GLN

ARG

ALA

4

THR

ALA

ARG

LYS

TYR

ASN

ILE

HIS

ARG

5

GLN

ILE

GLN

LYS

TRP

LEU

GLN

CYS

GLU

SER

6

ASN

LEU

ARG

SER

VAL

ALA

ASN

Entity 2, 5'-D(*TP*GP*AP*GP*GP*CP*GP*TP*CP*AP*AP*C)-3' 12 residues - Formula weight is not available

1

DT

DG

DA

DG

DC

DG

DT

DC

DA

2

DA

DC

Entity 3, 5'-D(*GP*TP*TP*GP*AP*CP*GP*CP*CP*TP*CP*A)-3' 12 residues - Formula weight is not available

1

DG

DT

DG

DA

DC

DG

DC

DT

2

DC

DA

Samples:

sample_1: brinker CG9653-PA, [U-15N], 1 mM; 5'-D(*TP*GP*AP*GP*GP*CP*GP*TP*CP*AP*AP*C)-3' 1 mM; 5'-D(*GP*TP*TP*GP*AP*CP*GP*CP*CP*TP*CP*A)-3' 1 mM; NaCl 10 mM; potassium phosphate 5 mM; TCEP 5 mM; NaN3 0.02%; H2O 95%; D2O 5%

sample_2: brinker CG9653-PA, [U-13C; U-15N], 1 mM; 5'-D(*TP*GP*AP*GP*GP*CP*GP*TP*CP*AP*AP*C)-3' 1 mM; 5'-D(*GP*TP*TP*GP*AP*CP*GP*CP*CP*TP*CP*A)-3' 1 mM; NaCl 10 mM; potassium phosphate 5 mM; TCEP 5 mM; NaN3 0.02%; H2O 95%; D2O 5%

sample_3: brinker CG9653-PA, [U-13C; U-15N], 0.35 mM; 5'-D(*TP*GP*AP*GP*GP*CP*GP*TP*CP*AP*AP*C)-3' 0.35 mM; 5'-D(*GP*TP*TP*GP*AP*CP*GP*CP*CP*TP*CP*A)-3' 0.35 mM; NaCl 10 mM; potassium phosphate 20 mM; DTT 2 mM; NaN3 0.02%; Pf1-phages 25 mg/mL; H2O 95%; D2O 5%

sample_cond_1: ionic strength: 10 mM; pH: 5.8; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 15N-separated NOESY	not available	not available	not available
3D 13C-separated NOESY	not available	not available	not available
3D dq-HNHA	not available	not available	not available
3D dq-HAHB	not available	not available	not available
2D HNCG	not available	not available	not available
2D HN(CO)CG	not available	not available	not available
2D 13C-selected/12C,14N-selected NOESY	not available	not available	not available
DSSE	not available	not available	not available
J-modulated-13C-HSQC	not available	not available	not available

Software:

xwinnmr v2.6 - collection

NMRPipe v2.2 - processing

PIPP v4.3.2 - data analysis

HADDOCK v1.2 - refinement

NMR spectrometers:

Bruker DRX 800 MHz

BMRB	7134
PDB	2GLO
DBJ	BAA76710
GB	AAD22080 AAF46251 ACD81876 ACK77656 EDV34122
REF	NP_511069 XP_001963673 XP_001978531 XP_002022676 XP_002043219