BMRB Entry 17399

Name: Structure of a novel CBM3 lacking the calcium-binding site
Published: 2011-12-20

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PDB ID: 2l8a
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR17399
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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:

Structure of a novel CBM3 lacking the calcium-binding site

Deposition date:

2011-01-07

Original release date:

2011-12-20

Authors:

Paiva, Joice; Meza, Andreia; Sforca, Mauricio; Navarro, Rodrigo; Neves, Jorge; Santos, Camila; Murakami, Mario; Zeri, Ana

Citation:

Citation: Santos, Camila; Paiva, Joice; Sforca, Mauricio; Neves, Jorge; Navarro, Rodrigo; Cota, Junio; Akao, Patricia; Hoffmam, Zaira; Meza, Andreia; Smetana, Juliana; Nogueira, Maria; Polikarpov, Igor; Neto, Jose; Squina, Fabio; Ward, Richard; Ruller, Roberto; Zeri, Ana; Murakami, Mario. "Dissecting structure-function-stability relationships of a thermostable GH5-CBM3 cellulase from Bacillus subtilis 168" Biochem. J. 441, 95-104.
PubMed: 21880019

Assembly members:

Assembly members:
entity, polymer, 149 residues, 16717.734 Da.

Natural source:

Natural source: Common Name: Bacillus subtilis Taxonomy ID: 1423 Superkingdom: Bacteria Kingdom: not available Genus/species: Bacillus subtilis

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET28

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity: MASISVQYRAGDGSMNSNQI RPQLQIKNNGNTTVDLKDVT ARYWYKAKNKGQNFDCDYAQ IGCGNVTHKFVTLHKPKQGA DTYLELGFKNGTLAPGASTG NIQLRLHNDDWSNYAQSGDY SFFKSNTFKTTKKITLYDQG KLIWGTEPN

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	583
15N chemical shifts	147
1H chemical shifts	917

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	CBM3	1

Entities:

Entity 1, CBM3 149 residues - 16717.734 Da.

1

MET

ALA

SER

ILE

SER

VAL

GLN

TYR

ARG

ALA

2

GLY

ASP

GLY

SER

MET

ASN

SER

ASN

GLN

ILE

3

ARG

PRO

GLN

LEU

GLN

ILE

LYS

ASN

GLY

4

ASN

THR

VAL

ASP

LEU

LYS

ASP

VAL

THR

5

ALA

ARG

TYR

TRP

TYR

LYS

ALA

LYS

ASN

LYS

6

GLY

GLN

ASN

PHE

ASP

CYS

ASP

TYR

ALA

GLN

7

ILE

GLY

CYS

GLY

ASN

VAL

THR

HIS

LYS

PHE

8

VAL

THR

LEU

HIS

LYS

PRO

LYS

GLN

GLY

ALA

9

ASP

THR

TYR

LEU

GLU

LEU

GLY

PHE

LYS

ASN

10

GLY

THR

LEU

ALA

PRO

GLY

ALA

SER

THR

GLY

11

ASN

ILE

GLN

LEU

ARG

LEU

HIS

ASN

ASP

12

TRP

SER

ASN

TYR

ALA

GLN

SER

GLY

ASP

TYR

13

SER

PHE

LYS

SER

ASN

THR

PHE

LYS

THR

14

THR

LYS

ILE

THR

LEU

TYR

ASP

GLN

GLY

15

LYS

LEU

ILE

TRP

GLY

THR

GLU

PRO

ASN

Samples:

sample_1: cbm, [U-99% 15N], 0.3 mM; H2O, relative abundance, 95%; D2O, relative abundance, 5%

sample_2: cbm, [U-100% 13C; U-100% 15N], 0.3 mM; H2O, relative abundance, 95%; D2O, relative abundance, 5%

sample_3: cbm, [U-100% 13C; U-100% 15N], 0.3 mM; D2O, relative abundance, 5%

sample_conditions_1: ionic strength: 70 mM; pH: 7.2; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_3	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_3	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_1	isotropic	sample_conditions_1

Software:

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

NMRView v5, Johnson, One Moon Scientific - chemical shift assignment, chemical shift calculation, peak picking

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

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

NMR spectrometers:

Varian INOVA 600 MHz

PDB	2L8A
DBJ	BAA00859 BAI85501 BAL46915 GAK81525
EMBL	CAA28392 CAA47429 CAA82317 CAA97610 CAB13696
GB	AAC02536 AAK39540 AAK94871 AAO63626 AAV34758
PRF	2106121A
REF	NP_389695 WP_003231540 WP_014479947 WP_015251994 WP_015383776
SP	P10475 P23549
AlphaFold	P10475 P23549