BMRB Entry 30523

Name: Solution structure of the large extracellular loop of FtsX in Streptococcus pneumoniae
Published: 2019-02-05

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PDB ID: 6mk7
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR30523
MolProbity Validation Chart

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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Solution structure of the large extracellular loop of FtsX in Streptococcus pneumoniae PubMed: 30696736

Deposition date: 2018-09-25 Original release date: 2019-02-05

Authors: Edmonds, K.; Fu, Y.; Wu, H.; Rued, B.; Bruce, K.; Winkler, M.; Giedroc, D.

Citation: Rued, B.; Alcorlo, M.; Edmonds, K.; Martinez-Caballero, S.; Straume, D.; Fu, Y.; Bruce, K.; Wu, H.; Havarstein, L.; Hermoso, J.; Winkler, M.; Giedroc, D.. "Structure of the Large Extracellular Loop of FtsX and Its Interaction with the Essential Peptidoglycan Hydrolase PcsB in Streptococcus pneumoniae" MBio 10, e02622-e02622 (2019).

Assembly members:
entity_1, polymer, 126 residues, 14013.403 Da.

Natural source: Common Name: Streptococcus pneumoniae Taxonomy ID: 373153 Superkingdom: Bacteria Kingdom: Streptococcus Genus/species: pneumoniae not available

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

Entity Sequences (FASTA):
entity_1: GAMATAKLATDIENNVRVVV YIRKDVEDNSQTIEKEGQTV TNNDYHKVYDSLKNMSTVKS VTFSSKEEQYEKLTEIMGDN WKIFEGDANPLYDAYIVEAN APNDVKTIAEDAKKIEGVSE VQDGGA

Data sets:

assigned_chemical_shifts
RDCs
- RDC_list_1
assigned_chemical_shifts
- assigned_chemical_shifts_1
heteronucl_NOEs
- heteronuclear_noe_list_1
heteronucl_T1_relaxation
- heteronuclear_T1_list_1
heteronucl_T2_relaxation
- heteronuclear_T2_list_600
- heteronuclear_T2_list_800
spectral_peak_list

Data type	Count
13C chemical shifts	541
15N chemical shifts	134
1H chemical shifts	847
T1 relaxation values	115
T2 relaxation values	242
heteronuclear NOE values	121
residual dipolar couplings	121

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 126 residues - 14013.403 Da.

1

GLY

ALA

MET

ALA

THR

ALA

LYS

LEU

ALA

THR

2

ASP

ILE

GLU

ASN

VAL

ARG

VAL

3

TYR

ILE

ARG

LYS

ASP

VAL

GLU

ASP

ASN

SER

4

GLN

THR

ILE

GLU

LYS

GLU

GLY

GLN

THR

VAL

5

THR

ASN

ASP

TYR

HIS

LYS

VAL

TYR

ASP

6

SER

LEU

LYS

ASN

MET

SER

THR

VAL

LYS

SER

7

VAL

THR

PHE

SER

LYS

GLU

GLN

TYR

8

GLU

LYS

LEU

THR

GLU

ILE

MET

GLY

ASP

ASN

9

TRP

LYS

ILE

PHE

GLU

GLY

ASP

ALA

ASN

PRO

10

LEU

TYR

ASP

ALA

TYR

ILE

VAL

GLU

ALA

ASN

11

ALA

PRO

ASN

ASP

VAL

LYS

THR

ILE

ALA

GLU

12

ASP

ALA

LYS

ILE

GLU

GLY

VAL

SER

GLU

13

VAL

GLN

ASP

GLY

ALA

Samples:

sample_1: FtsX extracellular loop 1, [U-99% 13C; U-99% 15N], 0.7 mM; H2O 90%; D2O, [U-99% 2H], 10%; potassium phosphate 50 mM; sodium chloride 50 mM; DSS 0.2 mM

sample_2: FtsX extracellular loop 1, [U-99% 13C; U-99% 15N], 0.7 mM; D2O, [U-99% 2H], 100%; potassium phosphate 50 mM; sodium chloride 50 mM

sample_3: FtsX extracellular loop 1, [U-99% 13C; U-99% 15N], 0.4 mM; H2O 90%; D2O, [U-99% 2H], 10%; potassium phosphate 50 mM; sodium chloride 50 mM; DSS 0.2 mM; Pf1 phage 20 mg/mL

sample_conditions_1: ionic strength: 100 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_2	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D HCCH-COSY	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_2	isotropic	sample_conditions_1
2D IPAP 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D IPAP 1H-15N HSQC	sample_3	anisotropic	sample_conditions_1
2D HBCBCGCDHE	sample_2	isotropic	sample_conditions_1
2D HBCBCGCDCEHE	sample_2	isotropic	sample_conditions_1
HN hNOE	sample_2	isotropic	sample_conditions_1
pseudo 3D T1	sample_2	isotropic	sample_conditions_1
pseudo 3D T2	sample_2	isotropic	sample_conditions_1
HN CPMG	sample_2	isotropic	sample_conditions_1
HN CPMG	sample_2	isotropic	sample_conditions_1

Software:

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

Analysis, CCPN - chemical shift assignment, peak picking

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

VNMRJ, Varian - collection

TALOS, Cornilescu, Delaglio and Bax - data analysis

SPARKY, Goddard - peak picking

NMR spectrometers:

Varian INOVA 600 MHz
Varian INOVA 800 MHz

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