BMRB Entry 5791

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PDB ID: 1osl
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR5791
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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:

Solution structure of a dimeric lactose DNA-binding domain complexed to a nonspecific DNA sequence

Deposition date:

2003-05-01

Original release date:

2004-10-18

Authors:

Kalodimos, C.; Bonvin, A.; Boelens, R.; Kaptein, R.

Citation:

Citation: Kalodimos, C.; Biris, N.; Bonvin, A.; Levandoski, M.; Guennuegues, M.; Boelens, R.; Kaptein, R.. "Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes " Science 305, 386-389 (2004).
PubMed: 15256668

Assembly members:

Assembly members:
Lactose operon repressor, polymer, 62 residues, Formula weight is not available
Binding DNA, polymer, 9 residues, Formula weight is not available
Binding DNA, polymer, 9 residues, Formula weight is not available

Natural source:

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

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: PET-HP62-V52C

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Lactose operon repressor: MKPVTLYDVAEYAGVSYQTV SRVVNQASHVSAKTREKVEA AMAELNYIPNRCAQQLAGKQ SL
Binding DNA: CGATAAGAT
Binding DNA: ATCTTATCG

Data sets:

assigned_chemical_shifts

Data type	Count
13C chemical shifts	117
1H chemical shifts	575
15N chemical shifts	69

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	lactose repressor chain A	1
2	lactose repressor chain B	1
3	BINDING DNA chain C	2
4	BINDING DNA chain D	3

Entities:

Entity 1, lactose repressor chain A 62 residues - Formula weight is not available

1

MET

LYS

PRO

VAL

THR

LEU

TYR

ASP

VAL

ALA

2

GLU

TYR

ALA

GLY

VAL

SER

TYR

GLN

THR

VAL

3

SER

ARG

VAL

ASN

GLN

ALA

SER

HIS

VAL

4

SER

ALA

LYS

THR

ARG

GLU

LYS

VAL

GLU

ALA

5

ALA

MET

ALA

GLU

LEU

ASN

TYR

ILE

PRO

ASN

6

ARG

CYS

ALA

GLN

LEU

ALA

GLY

LYS

GLN

7

SER

LEU

Entity 2, BINDING DNA chain C 9 residues - Formula weight is not available

1

DC

DG

DA

DT

DA

DG

DA

DT

Entity 3, BINDING DNA chain D 9 residues - Formula weight is not available

1

DA

DT

DC

DT

DA

DT

DC

DG

Samples:

sample_1: Lactose operon repressor, [U-15N; U-13C], 4 mM; Binding DNA, [U-15N; U-13C], 2 mM; Binding DNA, [U-15N; U-13C], 2 mM; KPI 60 mM; KCL 400 mM; H2O 90%; D2O 10%

sample_cond_1: pH: 5.8 na; temperature: 300 K; ionic strength: 460 mM; pressure: 1 atm

Experiments:

Name	Sample	Sample state	Sample conditions
3D 15N-separated NOESY	sample_1	not available	sample_cond_1
3D 13C-separated NOESY	sample_1	not available	sample_cond_1
13C-15N double-half noesy filter	sample_1	not available	sample_cond_1

Software:

XWINNMR v3.0 - collection

NMRPipe v2.1 - processing

NMRVIEW v5.0.3 - data analysis

CNS v1.1 - structure solution, refinement

NMR spectrometers:

Bruker DRX 750 MHz

BMRB	1066 127 1494 1552 32 4813 5345 661 736 848 849 96
PDB	1CJG 1EFA 1JWL 1JYE 1JYF 1L1M 1LBG 1LBH 1LBI 1LCC 1LCD 1LQC 1OSL 2KEI 2KEJ 2KEK 3EDC
DBJ	BAB20667 BAB33821 BAD00175 BAD20286 BAD20288
EMBL	CAA07594 CAA07597 CAA11118 CAA11119 CAA11120
GB	AAA24052 AAA56744 AAA56768 AAA57088 AAA57091
REF	NP_286086 NP_414879 WP_000718174 WP_000805876 WP_000805884
SP	P03023
AlphaFold	P03023