BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 19169

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

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

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

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

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

Data sets:
Data typeCount
13C chemical shifts669
15N chemical shifts163
1H chemical shifts1042

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1PG_21751

Entities:

Entity 1, PG_2175 156 residues - 17048.441 Da.

1   METSERLEUASNTHRTYRALAGLNLEUPRO
2   ALAVALSERLEULYSASNILEGLUGLYLYS
3   THRVALGLNTHRASNLYSLEUGLUASNALA
4   GLYLYSPROMETILEILESERPHEPHEALA
5   THRASNCYSLYSPROCYSLEUARGGLULEU
6   LYSALAILEGLNGLUVALTYRALAASPTRP
7   GLNASPGLUTHRGLYVALARGLEUILEALA
8   VALSERILEASPGLUGLYGLNASNALAGLN
9   LYSVALLYSPROLEUALAASPGLYASNGLY
10   TRPGLUTYRGLUVALLEULEUASPSERASN
11   GLYASPPHELYSARGALAMETASNVALSER
12   LEUILEPROALAVALPHEILEVALASPGLY
13   ASNGLYLYSILEVALTYRASNHISTHRGLY
14   TYRTHRGLUGLYGLYGLUALAGLULEUILE
15   LYSLYSVALARGGLULEUVALLYSGLUGLY
16   HISHISHISHISHISHIS

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:

NameSampleSample stateSample conditions
15N HSQCsample_1isotropicsample_conditions_1
15N NOESY-HSQCsample_1isotropicsample_conditions_1
13C HSQCsample_2isotropicsample_conditions_1
aromatic 13C HSQCsample_2isotropicsample_conditions_1
13C NOESY-HSQCsample_2isotropicsample_conditions_1
13C aromatic NOESY-HSQCsample_2isotropicsample_conditions_1
HNCOsample_1isotropicsample_conditions_1
HNCACOsample_1isotropicsample_conditions_1
HNCAsample_1isotropicsample_conditions_1
HNCOCAsample_1isotropicsample_conditions_1
HNCACBsample_1isotropicsample_conditions_1
CBCACONHsample_1isotropicsample_conditions_1

Software:

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

ARIA v2.3, Linge, O, . - 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

Related Database Links:

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