BMRB Entry 19169

Name: Solution structure of uncharacterized thioredoxin-like protein PG_2175 from Porphyromonas gingivalis
Published: 2013-05-13

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PDB ID: 2m72
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19169
MolProbity Validation Chart

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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:

Solution structure of uncharacterized thioredoxin-like protein PG_2175 from Porphyromonas gingivalis

Deposition date:

2013-04-16

Original release date:

2013-05-13

Authors:

Harris, R.; Ahmed, M.; Attonito, J.; Bonanno, J.; Chamala, S.; Chowdhury, S.; Evans, B.; Fiser, A.; Glenn, A.; Hammonds, J.; Hillerich, B.; Khafizov, K.; Lafleur, J.; Love, J.; Seidel, R.; Stead, M.; Girvin, M.; Almo, S.

Citation:

Citation: Harris, R.; Ahmed, M.; Attonito, J.; Bonanno, J.; Chamala, S.; Chowdhury, S.; Evans, B.; Fiser, A.; Glenn, A.; Hammonds, J.; Hillerich, B.; Khafizov, K.; Lafleur, J.; Love, J.; Seidel, R.; Stead, M.; Girvin, M.; Almo, S.. "Solution structure of uncharacterized thioredoxin-like protein PG_2175 from Porphyromonas gingivalis" To be published ., .-..

Assembly members:

Assembly members:
PG_2175, polymer, 156 residues, 17048.441 Da.

Natural source:

Natural source: Common Name: CFB group bacteria Taxonomy ID: 837 Superkingdom: Bacteria Kingdom: not available Genus/species: Porphyromonas gingivalis

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: modified pET26

Entity Sequences (FASTA):

Entity Sequences (FASTA):
PG_2175: MSLNTYAQLPAVSLKNIEGK TVQTNKLENAGKPMIISFFA TNCKPCLRELKAIQEVYADW QDETGVRLIAVSIDEGQNAQ KVKPLADGNGWEYEVLLDSN GDFKRAMNVSLIPAVFIVDG NGKIVYNHTGYTEGGEAELI KKVRELVKEGHHHHHH

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	669
15N chemical shifts	163
1H chemical shifts	1042

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	PG_2175	1

Entities:

Entity 1, PG_2175 156 residues - 17048.441 Da.

1

MET

SER

LEU

ASN

THR

TYR

ALA

GLN

LEU

PRO

2

ALA

VAL

SER

LEU

LYS

ASN

ILE

GLU

GLY

LYS

3

THR

VAL

GLN

THR

ASN

LYS

LEU

GLU

ASN

ALA

4

GLY

LYS

PRO

MET

ILE

SER

PHE

ALA

5

THR

ASN

CYS

LYS

PRO

CYS

LEU

ARG

GLU

LEU

6

LYS

ALA

ILE

GLN

GLU

VAL

TYR

ALA

ASP

TRP

7

GLN

ASP

GLU

THR

GLY

VAL

ARG

LEU

ILE

ALA

8

VAL

SER

ILE

ASP

GLU

GLY

GLN

ASN

ALA

GLN

9

LYS

VAL

LYS

PRO

LEU

ALA

ASP

GLY

ASN

GLY

10

TRP

GLU

TYR

GLU

VAL

LEU

ASP

SER

ASN

11

GLY

ASP

PHE

LYS

ARG

ALA

MET

ASN

VAL

SER

12

LEU

ILE

PRO

ALA

VAL

PHE

ILE

VAL

ASP

GLY

13

ASN

GLY

LYS

ILE

VAL

TYR

ASN

HIS

THR

GLY

14

TYR

THR

GLU

GLY

GLU

ALA

GLU

LEU

ILE

15

LYS

VAL

ARG

GLU

LEU

VAL

LYS

GLU

GLY

16

HIS

Samples:

sample_1: PG_2175, [U-100% 13C; U-100% 15N], 1 mM; D20 10%; H20 90%; Na acetate buffer 10 mM; DTT 3 mM; EDTA 0.1 mM

sample_2: PG_2175, [U-100% 13C; U-100% 15N], 1 mM; D20 100%; Na acetate buffer 10 mM; DTT 3 mM; EDTA 0.1 mM

sample_conditions_1: ionic strength: 10 mM; pH: 4.5; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 10 mM; pH: 4.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
15N HSQC	sample_1	isotropic	sample_conditions_1
15N NOESY-HSQC	sample_1	isotropic	sample_conditions_1
13C HSQC	sample_2	isotropic	sample_conditions_1
aromatic 13C HSQC	sample_2	isotropic	sample_conditions_1
13C NOESY-HSQC	sample_2	isotropic	sample_conditions_1
13C aromatic NOESY-HSQC	sample_2	isotropic	sample_conditions_1
HNCO	sample_1	isotropic	sample_conditions_1
HNCACO	sample_1	isotropic	sample_conditions_1
HNCA	sample_1	isotropic	sample_conditions_1
HNCOCA	sample_1	isotropic	sample_conditions_1
HNCACB	sample_1	isotropic	sample_conditions_1
CBCACONH	sample_1	isotropic	sample_conditions_1

Software:

CNS v1.21, Brunger A. T. et.al. - structure calcuation

ARIA v2.3, Linge, O'Donoghue and Nilges - structure calcuation

X-PLOR NIH v2.32, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

CCPN_Analysis v2.2, CCPN - chemical shift assignment, data analysis

MDDNMR v2.2, (MDDNMR) Orekhov, Jaravine, Kazimierczuk - collection, processing

MDDGUI, (MDDGUI) Lemak, Gutmanas, Chitayat, Karra, Fares, Sunnerhagen, Arrowsmith - collection, processing

NMRPipe v7.5, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SIDER, Hansen - data analysis

VNMRJ v2.2D, Varian - collection

TOPSPIN v2.1, Bruker Biospin - collection

MolProbity, Richardson - data analysis

NMR spectrometers:

Varian Inova 600 MHz
Bruker Avance 700 MHz

PDB	2M72
DBJ	BAG32639 BAK25401 GAP81477
GB	AAQ67124 AIJ34993 AKV65209 ALA94602 ALJ24608
REF	WP_004584609 WP_005874961 WP_012457260 WP_013816004 WP_018965155