BMRB Entry 30950

Name: Solution NMR structure of substrate bound peptidase domain from PCAT1
Published: 2021-12-31

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PDB ID: 7s5j
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30950
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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 NMR structure of substrate bound peptidase domain from PCAT1

Deposition date:

2021-09-10

Original release date:

2021-12-31

Authors:

Bhattacharya, S.; Palillo, A.

Citation:

Citation: Bhattacharya, S.; Palillo, A.. "Structural and dynamic studies of the peptidase domain from Clostridium thermocellum PCAT1" Protein Sci. 31, 498-512 (2022).
PubMed: 34865273

Assembly members:

Assembly members:
entity_1, polymer, 151 residues, 16635.389 Da.
entity_2, polymer, 24 residues, 2672.960 Da.

Natural source:

Natural source: Common Name: Acetivibrio thermocellus Taxonomy ID: 203119 Superkingdom: Bacteria Kingdom: not available Genus/species: Acetivibrio thermocellus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: PMCSG20

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: SNAMLRRLFKKKYVCVRQYD LTDAGAACLSSIAQYYGLKM SLAKIREMTGTDTQGTNAYG LIHAAKQLGFSAKGVKASKE DLLKDFRLPAIANVIVDNRL AHFVVIYSIKNRIITVADPG KGIVRYSMDDFCSIWTGGLV LLEPGEAFQKG
entity_2: LNIGRELTDEELMEMTGGST FSIQ

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	633
15N chemical shifts	154
1H chemical shifts	1021

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	2

Entities:

Entity 1, unit_1 151 residues - 16635.389 Da.

1

SER

ASN

ALA

MET

LEU

ARG

LEU

PHE

LYS

2

LYS

TYR

VAL

CYS

VAL

ARG

GLN

TYR

ASP

3

LEU

THR

ASP

ALA

GLY

ALA

CYS

LEU

SER

4

SER

ILE

ALA

GLN

TYR

GLY

LEU

LYS

MET

5

SER

LEU

ALA

LYS

ILE

ARG

GLU

MET

THR

GLY

6

THR

ASP

THR

GLN

GLY

THR

ASN

ALA

TYR

GLY

7

LEU

ILE

HIS

ALA

LYS

GLN

LEU

GLY

PHE

8

SER

ALA

LYS

GLY

VAL

LYS

ALA

SER

LYS

GLU

9

ASP

LEU

LYS

ASP

PHE

ARG

LEU

PRO

ALA

10

ILE

ALA

ASN

VAL

ILE

VAL

ASP

ASN

ARG

LEU

11

ALA

HIS

PHE

VAL

ILE

TYR

SER

ILE

LYS

12

ASN

ARG

ILE

THR

VAL

ALA

ASP

PRO

GLY

13

LYS

GLY

ILE

VAL

ARG

TYR

SER

MET

ASP

14

PHE

CYS

SER

ILE

TRP

THR

GLY

LEU

VAL

15

LEU

GLU

PRO

GLY

GLU

ALA

PHE

GLN

LYS

16

GLY

Entity 2, unit_2 24 residues - 2672.960 Da.

1

LEU

ASN

ILE

GLY

ARG

GLU

LEU

THR

ASP

GLU

2

GLU

LEU

MET

GLU

MET

THR

GLY

SER

THR

3

PHE

SER

ILE

GLN

Samples:

sample_1: C39 peptidase domain, [U-100% 13C; U-100% 15N], 140 uM; CtA(5-37) peptide 255 uM; sodium phosphate 50 mM; sodium chloride 150 mM; DTT 5 mM

sample_2: C39 peptidase domain 298 uM; CtA(5-37) peptide, [U-100% 13C; U-100% 15N], 184 uM; sodium phosphate 50 mM; sodium chloride 150 mM; DTT 5 mM

sample_conditions_1: ionic strength: 150 mM; pH: 7.0; pressure: 1 atm; temperature: 288 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 HNCA	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HCCH-COSY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
2D f1,f2 C13/N15 filtered NOESY	sample_1	isotropic	sample_conditions_1
2D f2 C13/N15 filtered NOESY	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_2	isotropic	sample_conditions_1
3D HNCA	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
3D HCCH-COSY	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_2	isotropic	sample_conditions_1

Software:

TopSpin v2.1, 3.5, Bruker Biospin - collection, processing

CARA v1.5, Keller and Wuthrich - chemical shift assignment, peak picking

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

ARIA v3.2, Linge, O'Donoghue and Nilges - refinement

NMR spectrometers:

Bruker AVANCE 500 MHz
Bruker AVANCE III HD 700 MHz
Bruker AVANCE 900 MHz
Bruker AVANCE III HD 800 MHz
Bruker AVANCE 800 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks