BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 25127

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

Data sets:
Data typeCount
1H chemical shifts1287
13C chemical shifts696
15N chemical shifts230

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity1

Entities:

Entity 1, entity 208 residues - 23706.646 Da.

Residues -2 and -1 are from a non-native purification tag

1   GLYHISMETGLNLYSTHRALAPHEILETRP
2   ASPLEUASPGLYTHRLEULEUASPSERTYR
3   GLUALAILELEUSERGLYILEGLUGLUTHR
4   PHEALAGLNPHESERILEPROTYRASPLYS
5   GLULYSVALARGGLUPHEILEPHELYSTYR
6   SERVALGLNASPLEULEUVALARGVALALA
7   GLUASPARGASNLEUASPVALGLUVALLEU
8   ASNGLNVALARGALAGLNSERLEUALAGLU
9   LYSASNALAGLNVALVALLEUMETPROGLY
10   ALAARGGLUVALLEUALATRPALAASPGLU
11   SERGLYILEGLNGLNPHEILETYRTHRHIS
12   LYSGLYASNASNALAPHETHRILELEULYS
13   ASPLEUGLYVALGLUSERTYRPHETHRGLU
14   ILELEUTHRSERGLNSERGLYPHEVALARG
15   LYSPROSERPROGLUALAALATHRTYRLEU
16   LEUASPLYSTYRGLNLEUASNSERASPASN
17   THRTYRTYRILEGLYASPARGTHRLEUASP
18   VALGLUPHEALAGLNASNSERGLYILEGLN
19   SERILEASNPHELEUGLUSERTHRTYRGLU
20   GLYASNHISARGILEGLNALALEUALAASP
21   ILESERARGILEPHEGLUTHRLYS

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:

NameSampleSample stateSample conditions
5D APSY-HACACONHsample_1isotropicsample_conditions_1
4D APSY-HACANHsample_1isotropicsample_conditions_1
4D APSY-HNCOCAsample_1isotropicsample_conditions_1
4D APSY-HNCACOsample_1isotropicsample_conditions_1
5D APSY-CBCACONHsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_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