BMRB Entry 16428

Name: The structure of the KlcA and ArdB proteins show a novel fold and antirestriction activity against Type I DNA restriction systems in vivo but not in vitro.
Published: 2010-02-02

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PDB ID: 2kmg
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR16428
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

The structure of the KlcA and ArdB proteins show a novel fold and antirestriction activity against Type I DNA restriction systems in vivo but not in vitro.

Deposition date:

2009-07-28

Original release date:

2010-02-02

Authors:

Serfiotis-Mitsa, Dimitra; Herbert, Andrew; Roberts, Gareth; Soares, Dinesh; White, John; Blakely, Garry; Uhrin, Dusan; Dryden, David

Citation:

Citation: Serfiotis-Mitsa, Dimitra; Herbert, Andrew; Roberts, Gareth; Soares, Dinesh; White, John; Blakely, Garry; Uhrin, Dusan; Dryden, David. "The structure of the KlcA and ArdB proteins reveals a novel fold and antirestriction activity against Type I DNA restriction systems in vivo but not in vitro." Nucleic Acids Res. 38, 1723-1737 (2010).
PubMed: 20007596

Assembly members:

Assembly members:
KlcA and ArdB proteins, polymer, 142 residues, Formula weight is not available

Natural source:

Natural source: Common Name: B. pertussis Taxonomy ID: 520 Superkingdom: Bacteria Kingdom: not available Genus/species: Bordetella pertussis

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET-24a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
KlcA and ArdB proteins: MNTEEQPVTASLVAEAQRLD FLPTYFGPRLMMRGEALVYA WMRRLCERYNGAYWHYYALS DGGFYMAPDLAGRLEIEVNG NGFRGELSADAAGIVATLFA LGQLAAEIADTDAADALIDR YHFLRGFAAGHPEAAAIYRA ID

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
RDCs
- RDC_list_1

Data type	Count
13C chemical shifts	559
15N chemical shifts	149
1H chemical shifts	897
residual dipolar couplings	110

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	KlcA and ArdB proteins	1

Entities:

Entity 1, KlcA and ArdB proteins 142 residues - Formula weight is not available

1

MET

ASN

THR

GLU

GLN

PRO

VAL

THR

ALA

2

SER

LEU

VAL

ALA

GLU

ALA

GLN

ARG

LEU

ASP

3

PHE

LEU

PRO

THR

TYR

PHE

GLY

PRO

ARG

LEU

4

MET

ARG

GLY

GLU

ALA

LEU

VAL

TYR

ALA

5

TRP

MET

ARG

LEU

CYS

GLU

ARG

TYR

ASN

6

GLY

ALA

TYR

TRP

HIS

TYR

ALA

LEU

SER

7

ASP

GLY

PHE

TYR

MET

ALA

PRO

ASP

LEU

8

ALA

GLY

ARG

LEU

GLU

ILE

GLU

VAL

ASN

GLY

9

ASN

GLY

PHE

ARG

GLY

GLU

LEU

SER

ALA

ASP

10

ALA

GLY

ILE

VAL

ALA

THR

LEU

PHE

ALA

11

LEU

GLY

GLN

LEU

ALA

GLU

ILE

ALA

ASP

12

THR

ASP

ALA

ASP

ALA

LEU

ILE

ASP

ARG

13

TYR

HIS

PHE

LEU

ARG

GLY

PHE

ALA

GLY

14

HIS

PRO

GLU

ALA

ILE

TYR

ARG

ALA

15

ILE

ASP

Samples:

sample_1: KlcA, [U-98% 13C; U-98% 15N], 0.7 mM; sodium acetate, [U-100% 2H], 20 mM; sodium azide 0.05%; H2O 90%; D2O 10%

sample_2: KlcA, [U-98% 15N], 0.7 mM; sodium acetate, [U-100% 2H], 20 mM; sodium azide 0.05%; Pf1 phage 6.25 mg; H2O 90%; D2O 10%

sample_3: KlcA, [U-98% 15N], 0.7 mM; sodium acetate, [U-100% 2H], 20 mM; sodium azide 0.05%; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 20 mM; pH: 6.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D CBCANH	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCACO	sample_1	isotropic	sample_conditions_1
3D HBHANH	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC (Aromatic Selective)	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D C(CCO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
2D HBCBCGCDHD	sample_1	isotropic	sample_conditions_1
2D HBCBCGCDCEHE	sample_1	isotropic	sample_conditions_1
T1	sample_3	isotropic	sample_conditions_1
T2	sample_3	isotropic	sample_conditions_1
Heteronuclear NOE	sample_3	isotropic	sample_conditions_1
IPAP for RDC measurement	sample_2	anisotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1

Software:

TOPSPIN v1.3, Bruker Biospin - collection

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

CNS v1.1, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

ANALYSIS v1.0.15, CCPN - chemical shift assignment, data analysis, peak picking

AZARA v2.7, Boucher - processing

ProcheckNMR v3.5, Laskowski and MacArthur - Structure Validation

WhatIF, Vriend - Structure Validation

TALOS, Cornilescu, Delaglio and Bax - data analysis

NMR spectrometers:

Bruker Avance 800 MHz
Bruker Avance 600 MHz

EMBL	BAF33451.1
UNP	Q08L07
PDB	2KMG
DBJ	BAF33451
REF	WP_011666376 YP_787932
AlphaFold	Q08L07