BMRB Entry 30081

Name: The structure of chaperone SecB in complex with unstructured PhoA binding site a
Published: 2016-08-18

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PDB ID: 5jtm
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30081
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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: The structure of chaperone SecB in complex with unstructured PhoA binding site a PubMed: 27501151

Deposition date: 2016-05-09 Original release date: 2016-08-18

Authors: Huang, C.; Saio, T.; Rossi, P.; Kalodimos, C.

Citation: Huang, C.; Saio, T.; Rossi, P.; Kalodimos, C.. "Structural basis for the antifolding activity of a molecular chaperone" Nature 537, 202-206 (2016).

Assembly members:
Protein-export protein SecB, polymer, 155 residues, 17287.266 Da.
Alkaline phosphatase, polymer, 25 residues, 2743.329 Da.

Natural source: Common Name: enterobacteria Taxonomy ID: 585055 Superkingdom: not available Kingdom: Escherichia Genus/species: coli not available

Experimental source: Production method: recombinant technology Host organism: Escherichia coli BL21(DE3)

Entity Sequences (FASTA):
Protein-export protein SecB: MSEQNNTEMTFQIQRIYTKD ISFEAPNAPHVFQKDWQPEV KLDLDTASSQLADDVYEVVL RVTVTASLGEETAFLCEVQQ GGIFSIAGIEGTQMAHCLGA YCPNILFPYARECITSMVSR GTFPQLNLAPVNFDALFMNY LQQQAGEGTEEHQDA
Alkaline phosphatase: MKQSTIALALLPLLFTPVTK ARTPE

Data sets:

assigned_chemical_shifts

Data type	Count
13C chemical shifts	2334
15N chemical shifts	618
1H chemical shifts	2138

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1, chain 1	1
2	entity_1, chain 2	1
3	entity_1, chain 3	1
4	entity_1, chain 4	1
5	entity_2, chain 1	2
6	entity_2, chain 2	2
7	entity_2, chain 3	2
8	entity_2, chain 4	2

Entities:

Entity 1, entity_1, chain 1 155 residues - 17287.266 Da.

1

MET

SER

GLU

GLN

ASN

THR

GLU

MET

THR

2

PHE

GLN

ILE

GLN

ARG

ILE

TYR

THR

LYS

ASP

3

ILE

SER

PHE

GLU

ALA

PRO

ASN

ALA

PRO

HIS

4

VAL

PHE

GLN

LYS

ASP

TRP

GLN

PRO

GLU

VAL

5

LYS

LEU

ASP

LEU

ASP

THR

ALA

SER

GLN

6

LEU

ALA

ASP

VAL

TYR

GLU

VAL

LEU

7

ARG

VAL

THR

VAL

THR

ALA

SER

LEU

GLY

GLU

8

GLU

THR

ALA

PHE

LEU

CYS

GLU

VAL

GLN

9

GLY

ILE

PHE

SER

ILE

ALA

GLY

ILE

GLU

10

GLY

THR

GLN

MET

ALA

HIS

CYS

LEU

GLY

ALA

11

TYR

CYS

PRO

ASN

ILE

LEU

PHE

PRO

TYR

ALA

12

ARG

GLU

CYS

ILE

THR

SER

MET

VAL

SER

ARG

13

GLY

THR

PHE

PRO

GLN

LEU

ASN

LEU

ALA

PRO

14

VAL

ASN

PHE

ASP

ALA

LEU

PHE

MET

ASN

TYR

15

LEU

GLN

ALA

GLY

GLU

GLY

THR

GLU

16

GLU

HIS

GLN

ASP

ALA

Entity 2, entity_2, chain 1 25 residues - 2743.329 Da.

1

MET

LYS

GLN

SER

THR

ILE

ALA

LEU

ALA

LEU

2

LEU

PRO

LEU

PHE

THR

PRO

VAL

THR

LYS

3

ALA

ARG

THR

PRO

GLU

Samples:

sample_1: PhoA binding site a, [U-100% 13C; U-100% 15N], 300 uM; SecB, [U-100% 13C; U-100% 15N], 300 uM; potassium chloride 150 uM; potassium phosphate 50 uM; sodium phosphate 50 uM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 150 mM; pH: 7; pressure: 1 atm; temperature: 301 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1

Software:

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRView, Johnson, One Moon Scientific - chemical shift assignment

NMR spectrometers:

Bruker AvanceIII 700 MHz
Varian INOVA 900 MHz

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts