BMRB Entry 30322

Name: NMR solution structure of a-lytic protease using two 4D-spectra
Published: 2018-01-29

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PDB ID: 5wot
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR30322
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR solution structure of a-lytic protease using two 4D-spectra

Deposition date:

2017-08-03

Original release date:

2018-01-29

Authors:

Evangelidis, T.; Nerli, S.; Sgourakis, N.; Tripsianes, K.

Citation:

Citation: Evangelidis, T.; Nerli, S.; Novacek, J.; Brereton, A.; Karplus, P.; Dotas, R.; Venditti, V.; Sgourakis, N.; Tripsianes, K.. "Automated NMR resonance assignments and structure determination using a minimal set of 4D spectra" Nat. Commun. 9, 384-384 (2018).
PubMed: 29374165

Assembly members:

Assembly members:
Alpha-lytic protease, polymer, 198 residues, 19875.131 Da.

Natural source:

Natural source: Common Name: Lysobacter enzymogenes Taxonomy ID: 69 Superkingdom: Bacteria Kingdom: not available Genus/species: Lysobacter enzymogenes

Experimental source:

Experimental source: Production method: .

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Alpha-lytic protease: ANIVGGIEYSINNASLCSVG FSVTRGATKGFVTAGHCGTV NATARIGGAVVGTFAARVFP GNDRAWVSLTSAQTLLPRVA NGSSFVTVRGSTEAAVGAAV CRSGRTTGYQCGTITAKNVT ANYAEGAVRGLTQGNACMGR GDSGGSWITSAGQAQGVMSG GNVQSNGNNCGIPASQRSSL FERLQPILSQYGLSLVTG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1
- spectral_peak_list_2

Data type	Count
13C chemical shifts	540
15N chemical shifts	222
1H chemical shifts	1201

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 198 residues - 19875.131 Da.

1

ALA

ASN

ILE

VAL

GLY

ILE

GLU

TYR

SER

2

ILE

ASN

ALA

SER

LEU

CYS

SER

VAL

GLY

3

PHE

SER

VAL

THR

ARG

GLY

ALA

THR

LYS

GLY

4

PHE

VAL

THR

ALA

GLY

HIS

CYS

GLY

THR

VAL

5

ASN

ALA

THR

ALA

ARG

ILE

GLY

ALA

VAL

6

VAL

GLY

THR

PHE

ALA

ARG

VAL

PHE

PRO

7

GLY

ASN

ASP

ARG

ALA

TRP

VAL

SER

LEU

THR

8

SER

ALA

GLN

THR

LEU

PRO

ARG

VAL

ALA

9

ASN

GLY

SER

PHE

VAL

THR

VAL

ARG

GLY

10

SER

THR

GLU

ALA

VAL

GLY

ALA

VAL

11

CYS

ARG

SER

GLY

ARG

THR

GLY

TYR

GLN

12

CYS

GLY

THR

ILE

THR

ALA

LYS

ASN

VAL

THR

13

ALA

ASN

TYR

ALA

GLU

GLY

ALA

VAL

ARG

GLY

14

LEU

THR

GLN

GLY

ASN

ALA

CYS

MET

GLY

ARG

15

GLY

ASP

SER

GLY

SER

TRP

ILE

THR

SER

16

ALA

GLY

GLN

ALA

GLN

GLY

VAL

MET

SER

GLY

17

GLY

ASN

VAL

GLN

SER

ASN

GLY

ASN

CYS

18

GLY

ILE

PRO

ALA

SER

GLN

ARG

SER

LEU

19

PHE

GLU

ARG

LEU

GLN

PRO

ILE

LEU

SER

GLN

20

TYR

GLY

LEU

SER

LEU

VAL

THR

GLY

Samples:

sample_1: alpha-lytic protease protein, [U-13C; U-15N], 2.0 mM; sodium acetate 10 mM; NaCl 50 mM

sample_conditions_1: ionic strength: 50 mM; pH: 4.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
4D HC(CC-TOCSY(CO))NH	sample_1	isotropic	sample_conditions_1
4D 13C,15N edited HMQC-NOESY-HSQC	sample_1	isotropic	sample_conditions_1
4D 13C,13C edited HMQC-NOESY-HSQC	sample_1	isotropic	sample_conditions_1

Software:

4D-CHAINS, Evangelidis and Tripsianes - chemical shift assignment

CS-Rosetta, Shen, Vernon, Baker and Bax - data analysis, refinement, structure calculation

SPARKY, Goddard - peak picking

NMR spectrometers:

Bruker AvanceIII 950 MHz

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