BMRB Entry 19169
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19169
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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: 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
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 669 |
| 15N chemical shifts | 163 |
| 1H chemical shifts | 1042 |
Additional metadata:
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 | ILE | SER | PHE | 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 | 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 | GLY | GLU | ALA | GLU | LEU | ILE | ||||
| 15 | LYS | LYS | VAL | ARG | GLU | LEU | VAL | LYS | GLU | GLY | ||||
| 16 | HIS | HIS | HIS | HIS | HIS | 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, . - 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 |
Download simulated HSQC data in one of the following formats:
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