BMRB Entry 25127
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25127
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Title: NMR structure of a putative phosphoglycolate phosphatase (NP_346487.1) from Streptococcus pneumoniae TIGR4
Deposition date: 2014-08-04 Original release date: 2014-09-22
Authors: Jaudzems, Kristaps; Serrano, Pedro; Pedrini, Bill; Geralt, Michael; Wuthrich, Kurt
Citation: Jaudzems, Kristaps; Serrano, Pedro; Pedrini, Bill; Geralt, Michael; Wuthrich, Kurt. "NMR structure of a putative phosphoglycolate phosphatase (NP_346487.1) from Streptococcus pneumoniae TIGR4" To be Published ., .-..
Assembly members:
entity, polymer, 208 residues, 23706.646 Da.
Natural source: Common Name: firmicutes Taxonomy ID: 170187 Superkingdom: Bacteria Kingdom: not available Genus/species: Streptococcus pneumoniae
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
entity: GHMQKTAFIWDLDGTLLDSY
EAILSGIEETFAQFSIPYDK
EKVREFIFKYSVQDLLVRVA
EDRNLDVEVLNQVRAQSLAE
KNAQVVLMPGAREVLAWADE
SGIQQFIYTHKGNNAFTILK
DLGVESYFTEILTSQSGFVR
KPSPEAATYLLDKYQLNSDN
TYYIGDRTLDVEFAQNSGIQ
SINFLESTYEGNHRIQALAD
ISRIFETK
- assigned_chemical_shifts
| Data type | Count |
| 1H chemical shifts | 1287 |
| 13C chemical shifts | 696 |
| 15N chemical shifts | 230 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity | 1 |
Entities:
Entity 1, entity 208 residues - 23706.646 Da.
Residues -2 and -1 are from a non-native purification tag
| 1 | GLY | HIS | MET | GLN | LYS | THR | ALA | PHE | ILE | TRP | ||||
| 2 | ASP | LEU | ASP | GLY | THR | LEU | LEU | ASP | SER | TYR | ||||
| 3 | GLU | ALA | ILE | LEU | SER | GLY | ILE | GLU | GLU | THR | ||||
| 4 | PHE | ALA | GLN | PHE | SER | ILE | PRO | TYR | ASP | LYS | ||||
| 5 | GLU | LYS | VAL | ARG | GLU | PHE | ILE | PHE | LYS | TYR | ||||
| 6 | SER | VAL | GLN | ASP | LEU | LEU | VAL | ARG | VAL | ALA | ||||
| 7 | GLU | ASP | ARG | ASN | LEU | ASP | VAL | GLU | VAL | LEU | ||||
| 8 | ASN | GLN | VAL | ARG | ALA | GLN | SER | LEU | ALA | GLU | ||||
| 9 | LYS | ASN | ALA | GLN | VAL | VAL | LEU | MET | PRO | GLY | ||||
| 10 | ALA | ARG | GLU | VAL | LEU | ALA | TRP | ALA | ASP | GLU | ||||
| 11 | SER | GLY | ILE | GLN | GLN | PHE | ILE | TYR | THR | HIS | ||||
| 12 | LYS | GLY | ASN | ASN | ALA | PHE | THR | ILE | LEU | LYS | ||||
| 13 | ASP | LEU | GLY | VAL | GLU | SER | TYR | PHE | THR | GLU | ||||
| 14 | ILE | LEU | THR | SER | GLN | SER | GLY | PHE | VAL | ARG | ||||
| 15 | LYS | PRO | SER | PRO | GLU | ALA | ALA | THR | TYR | LEU | ||||
| 16 | LEU | ASP | LYS | TYR | GLN | LEU | ASN | SER | ASP | ASN | ||||
| 17 | THR | TYR | TYR | ILE | GLY | ASP | ARG | THR | LEU | ASP | ||||
| 18 | VAL | GLU | PHE | ALA | GLN | ASN | SER | GLY | ILE | GLN | ||||
| 19 | SER | ILE | ASN | PHE | LEU | GLU | SER | THR | TYR | GLU | ||||
| 20 | GLY | ASN | HIS | ARG | ILE | GLN | ALA | LEU | ALA | ASP | ||||
| 21 | ILE | SER | ARG | ILE | PHE | GLU | THR | LYS |
Samples:
sample_1: entity, [U-100% 13C; U-100% 15N], 1.5 ± 0.1 mM; D2O, [U-100% 2H], 5 ± 0.5 %; sodium azide 0.03 ± 0.01 %; sodium phosphate 20 ± 2 mM; sodium chloride 50 ± 2 mM; H2O 95%
sample_conditions_1: temperature: 298 K; pH: 6.5; pressure: 1 atm; ionic strength: 0.08 M
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 5D APSY-HACACONH | sample_1 | isotropic | sample_conditions_1 |
| 4D APSY-HACANH | sample_1 | isotropic | sample_conditions_1 |
| 4D APSY-HNCOCA | sample_1 | isotropic | sample_conditions_1 |
| 4D APSY-HNCACO | sample_1 | isotropic | sample_conditions_1 |
| 5D APSY-CBCACONH | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aromatic | sample_1 | isotropic | sample_conditions_1 |
Software:
CYANA v3.0, Guntert, Mumenthaler and Wuthrich - structure solution
OPAL, Luginbuhl, Guntert, Billeter and Wuthrich - refinement
TOPSPIN v2.1, Bruker Biospin - collection
CARA v1.9, Keller, Wuthrich - data analysis
UNIO-MATCH, Volk, Herrmann, Wuthrich - chemical shift assignment
UNIO-ATNOS-ASCAN, Fiorito, Herrmann, Guntert, Wuthrich - chemical shift assignment
UNIO-ATNOS-CANDID, Herrmann, Guntert, Wuthrich - peak picking, structure solution
NMR spectrometers:
- Bruker Avance 600 MHz
- Bruker Avance 800 MHz
Related Database Links:
| PDB | |
| EMBL | CAR69831 CBW33471 CBW35510 CBW37461 CCP31549 |
| GB | AAK76127 AAL00678 ABJ54930 ACA36863 ACB91283 |
| REF | NP_359467 WP_001172817 WP_001172820 WP_001172821 WP_001172822 |