BMRB Entry 30020

Name: The C-terminal domain of rice beta-galactosidase 1
Published: 2016-08-08

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PDB ID: 5iaz
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR30020
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: The C-terminal domain of rice beta-galactosidase 1 PubMed: 27451952

Deposition date: 2016-02-22 Original release date: 2016-08-08

Authors: Rimlumduan, T.; Hua, Y.-l.; Tanaka, T.; Ketudat-Cairns, J.R.

Citation: Rimlumduan, T.; Hua, Y.-l.; Tanaka, T.; Ketudat-Cairns, J.R.. "Structure of a plant beta-galactosidase C-terminal domain" Biochim. Biophys. Acta 1864, 1411-1418 (2016).

Assembly members:
entity_1, polymer, 122 residues, 13029.779 Da.

Natural source: Common Name: Rice Taxonomy ID: 39946 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Oryza sativa

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

Entity Sequences (FASTA):
entity_1: GSHMRTVSGVCADVSEYHPN IKNWQIESYGEPEFHTAKVH LKCAPGQTISAIKFASFGTP LGTCGTFQQGECHSINSNSV LERKCIGLERCVVAISPSNF GGDPCPEVMKRVAVEAVCST AA

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	444
15N chemical shifts	114
1H chemical shifts	775

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_1 122 residues - 13029.779 Da.

1

GLY

SER

HIS

MET

ARG

THR

VAL

SER

GLY

VAL

2

CYS

ALA

ASP

VAL

SER

GLU

TYR

HIS

PRO

ASN

3

ILE

LYS

ASN

TRP

GLN

ILE

GLU

SER

TYR

GLY

4

GLU

PRO

GLU

PHE

HIS

THR

ALA

LYS

VAL

HIS

5

LEU

LYS

CYS

ALA

PRO

GLY

GLN

THR

ILE

SER

6

ALA

ILE

LYS

PHE

ALA

SER

PHE

GLY

THR

PRO

7

LEU

GLY

THR

CYS

GLY

THR

PHE

GLN

GLY

8

GLU

CYS

HIS

SER

ILE

ASN

SER

ASN

SER

VAL

9

LEU

GLU

ARG

LYS

CYS

ILE

GLY

LEU

GLU

ARG

10

CYS

VAL

ALA

ILE

SER

PRO

SER

ASN

PHE

11

GLY

ASP

PRO

CYS

PRO

GLU

VAL

MET

LYS

12

ARG

VAL

ALA

VAL

GLU

ALA

VAL

CYS

SER

THR

13

ALA

Samples:

sample_1: D2O, [U-2H], 5%; H2O 95%; OsBGal1 Cter 0.5 mM; sodium chloride 100 mM; sodium phosphate 20 mM

sample_2: D2O, [U-2H], 100%; OsBGal1 Cter 0.54 mM; sodium chloride 100 mM; sodium phosphate 20 mM

sample_3: D2O, [U-2H], 5%; H2O 95%; OsBGal1 Cter, [U-100% 15N], 0.79 mM; sodium chloride 100 mM; sodium phosphate 20 mM

sample_4: D2O, [U-2H], 5%; H2O 95%; OsBGal1 Cter, [U-100% 13C; U-100% 15N], 0.5 mM; sodium chloride 100 mM; sodium phosphate 20 mM

sample_5: D2O, [U-2H], 5%; H2O 95%; OsBGal1 Cter, [U-10% 13C], 0.18 mM; sodium chloride 100 mM; sodium phosphate 20 mM

sample_conditions_1: ionic strength: 120 mM; pH: 7.4; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_3	isotropic	sample_conditions_1
3D HNHA	sample_3	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_4	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_4	isotropic	sample_conditions_1
3D HNCO	sample_4	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_4	isotropic	sample_conditions_1
3D HNCACB	sample_4	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_4	isotropic	sample_conditions_1
3D C(CO)NH	sample_4	isotropic	sample_conditions_1
3D HBCBCACOCAHA	sample_4	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_4	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_5	isotropic	sample_conditions_1

Software:

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

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

PIPP, Garrett - peak picking

ProcheckNMR, Laskowski and MacArthur - data analysis

X-PLOR vv3.1, Brunger - structure calculation

NMR spectrometers:

Varian UNITY INOVA 500 MHz
Bruker AVANCE DRX 800 MHz
Bruker AVANCE III 800 MHz

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