BMRB Entry 52129

Name: Solution Structure of RsgI9 CRE domain from C. thermocellum
Published: 2024-04-16

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PDB ID: 8u9o
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR52129
MolProbity Validation Chart

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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 RsgI9 CRE domain from C. thermocellum

Deposition date:

2023-09-15

Original release date:

2024-04-16

Authors:

Takayesu, Allen; Mahoney, Brendan; Clubb, Robert

Citation:

Citation: Takayesu, Allen; Mahoney, Brendan; Goring, Andrew; Jessup, Tobie; Ogorzalek Loo, Rachel; Loo, Joseph; Clubb, Robert. "Insight into the autoproteolysis mechanism of the RsgI9 anti-sigma factor from Clostridium thermocellum" Proteins 92, 946-958 (2024).
PubMed: 38597224

Assembly members:

Assembly members:
entity_1, polymer, 22 residues, Formula weight is not available
entity_2, polymer, 155 residues, Formula weight is not available

Natural source:

Natural source: Common Name: Clostridium thermocellum Taxonomy ID: 1515 Superkingdom: Bacteria Kingdom: not available Genus/species: Clostridium thermocellum

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET-29b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GRNVMLNNSSGSEYAYVSVD VN
entity_2: PSVEFTINSKHKVIVTSAIN QDASEVLDGLELKEKDLKSA LVMVLEKAESLGYISDDKNY VLVSMALNDKNKKTRDKREE KIDELKETIEQGIEALDNDT IVHRTVTVDLEERNKALENE LSMGRYYLYLEAKEKGMDIT IDEVKSSKISDLIEK

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	712
15N chemical shifts	177
1H chemical shifts	1015

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RsgI9 CRE (Chain A)	1
2	RsgI9 CRE (Chain B)	2

Entities:

Entity 1, RsgI9 CRE (Chain A) 22 residues - Formula weight is not available

1

GLY

ARG

ASN

VAL

MET

LEU

ASN

SER

2

GLY

SER

GLU

TYR

ALA

TYR

VAL

SER

VAL

ASP

3

VAL

ASN

Entity 2, RsgI9 CRE (Chain B) 155 residues - Formula weight is not available

1

PRO

SER

VAL

GLU

PHE

THR

ILE

ASN

SER

LYS

2

HIS

LYS

VAL

ILE

VAL

THR

SER

ALA

ILE

ASN

3

GLN

ASP

ALA

SER

GLU

VAL

LEU

ASP

GLY

LEU

4

GLU

LEU

LYS

GLU

LYS

ASP

LEU

LYS

SER

ALA

5

LEU

VAL

MET

VAL

LEU

GLU

LYS

ALA

GLU

SER

6

LEU

GLY

TYR

ILE

SER

ASP

LYS

ASN

TYR

7

VAL

LEU

VAL

SER

MET

ALA

LEU

ASN

ASP

LYS

8

ASN

LYS

THR

ARG

ASP

LYS

ARG

GLU

9

LYS

ILE

ASP

GLU

LEU

LYS

GLU

THR

ILE

GLU

10

GLN

GLY

ILE

GLU

ALA

LEU

ASP

ASN

ASP

THR

11

ILE

VAL

HIS

ARG

THR

VAL

THR

VAL

ASP

LEU

12

GLU

ARG

ASN

LYS

ALA

LEU

GLU

ASN

GLU

13

LEU

SER

MET

GLY

ARG

TYR

LEU

TYR

LEU

14

GLU

ALA

LYS

GLU

LYS

GLY

MET

ASP

ILE

THR

15

ILE

ASP

GLU

VAL

LYS

SER

LYS

ILE

SER

16

ASP

LEU

ILE

GLU

LYS

Samples:

sample_1: RsgI9 CRE, [U-13C; U-15N], 200 uM; sodium azide 0.03%; sodium phosphate 50 mM; sodium chloride 200 mM; D2O, [U-2H], 8%

sample_2: RsgI9 CRE, [U-13C; U-15N], 200 uM; sodium azide 0.03%; sodium phosphate 50 mM; sodium chloride 200 mM; D2O, [U-99% 2H], 100%

sample_conditions_1: ionic strength: 0.2 M; pH: 6.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N TROSY	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
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_1
2D 1H-1H COSY	sample_2	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HN(CA)CO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HN(CO)CACB	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HCCH-COSY	sample_2	isotropic	sample_conditions_1
3D HNHA	sample_1	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 aliphatic	sample_1	isotropic	sample_conditions_1
1H-15N heteronoe	sample_1	isotropic	sample_conditions_1

Software:

X-PLOR NIH v3.6 - structure solution

XIPP v1.21.7 - chemical shift assignment, peak picking

CARA - chemical shift assignment

TOPSPIN - collection, data analysis

NMRPipe - processing

Molmol - refinement

TALOS-N - geometry optimization

Procheck - refinement

UNIO - peak picking

NMRFAM-SPARKY - data analysis

NMR spectrometers:

Bruker AVANCE III 600 MHz
Bruker AVANCE NEO 800 MHz