BMRB Entry 11426

Name: Solution structure of SecDF periplasmic domain P4
Published: 2012-01-30

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PDB ID: 2rrn
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR11426
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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 SecDF periplasmic domain P4

Deposition date:

2011-01-30

Original release date:

2012-01-30

Authors:

Tanaka, Takeshi; Tsukazaki, Tomoya; Echizen, Yuka; Nureki, Osamu; Kohno, Toshiyuki

Citation:

Citation: Tsukazaki, Tomoya; Mori, Hiroyuki; Echizen, Yuka; Ishitani, Ryuichiro; Fukai, Shuya; Tanaka, Takeshi; Perederina, Anna; Vassylyev, Dmitry; Kohno, Toshiyuki; Maturana, Andres; Ito, Koreaki; Nureki, Osamu. "Structure and function of a membrane component SecDF that enhances protein export" Nature 474, 235-238 (2011).
PubMed: 21562494

Assembly members:

Assembly members:
entity, polymer, 92 residues, 10291.784 Da.

Natural source:

Natural source: Common Name: bacteria Taxonomy ID: 300852 Superkingdom: Bacteria Kingdom: not available Genus/species: Thermus thermophilus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pYE79

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity: MVGFNYSIDFTGGTAYTLRA EPNVEVETLRRFLEEKGFPG KEAVITQVQAPTAAYREFLV KLPPLSDERRLELERLFASE LKATVLASETVG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	380
15N chemical shifts	96
1H chemical shifts	610

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	periplasmic domain P4, residues 470-559	1

Entities:

Entity 1, periplasmic domain P4, residues 470-559 92 residues - 10291.784 Da.

1

MET

VAL

GLY

PHE

ASN

TYR

SER

ILE

ASP

PHE

2

THR

GLY

THR

ALA

TYR

THR

LEU

ARG

ALA

3

GLU

PRO

ASN

VAL

GLU

VAL

GLU

THR

LEU

ARG

4

ARG

PHE

LEU

GLU

LYS

GLY

PHE

PRO

GLY

5

LYS

GLU

ALA

VAL

ILE

THR

GLN

VAL

GLN

ALA

6

PRO

THR

ALA

TYR

ARG

GLU

PHE

LEU

VAL

7

LYS

LEU

PRO

LEU

SER

ASP

GLU

ARG

8

LEU

GLU

LEU

GLU

ARG

LEU

PHE

ALA

SER

GLU

9

LEU

LYS

ALA

THR

VAL

LEU

ALA

SER

GLU

THR

10

VAL

GLY

Samples:

sample_1: P4 domain, [U-13C; U-15N], 1 mM; TRIS 20 mM; sodium chloride 50 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 50 mM; pH: 6.5; pressure: 1 atm; temperature: 303 K

Experiments:

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

Software:

TOPSPIN, Bruker Biospin - collection

SPARKY, Goddard - chemical shift assignment

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

TALOS, Cornilescu, Delaglio and Bax - structure solution

ProcheckNMR, Laskowski and MacArthur - structure solution

NMR spectrometers:

Bruker Avance 500 MHz

PDB	2RRN 3AQP
DBJ	BAD70520
GB	AAS80693
REF	WP_011172795 YP_143963
SP	Q5SKE6
AlphaFold	Q5SKE6