BMRB Entry 16988

Name: Solution NMR Structure of a domain of adhesion exoprotein from Pediococcus pentosaceus, Northeast Structural Genomics Consortium Target PtR41O
Published: 2010-08-10

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PDB ID: 2kyw
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16988
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution NMR Structure of a domain of adhesion exoprotein from Pediococcus pentosaceus, Northeast Structural Genomics Consortium Target PtR41O

Deposition date:

2010-06-09

Original release date:

2010-08-10

Authors:

He, Yunfen; Eletsky, Alexander; Mills, Jeffrey; Wang, Huang; Ciccosanti, Colleen; Janjua, Haleema; Acton, Thomas; Xiao, Rong; Everett, John; Lee, Hsiau-Wei; Prestegard, James; Montelione, Gaetano; Szyperski, Thomas

Citation:

Citation: He, Yunfen; Eletsky, Alexander; Mills, Jeffrey; Wang, Huang; Ciccosanti, Colleen; Janjua, Haleema; Acton, Thomas; Xiao, Rong; Everett, John; Lee, Hsiau-Wei; Prestegard, James; Montelione, Gaetano; Szyperski, Thomas. "Solution NMR Structure of a domain of adhesion exoprotein from Pediococcus pentosaceus, Northeast Structural Genomics Consortium Target PtR41O" .

Assembly members:

Assembly members:
PtR41O, polymer, 87 residues, 9309.011 Da.

Natural source:

Natural source: Common Name: Pediococcus pentosaceus Taxonomy ID: 1255 Superkingdom: Bacteria Kingdom: not available Genus/species: Pediococcus pentosaceus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET21

Entity Sequences (FASTA):

Entity Sequences (FASTA):
PtR41O: MDEDATITYVDDDKGGAQVG DIVTVTGKTDDSTTYTVTIP DGYEYVGTDGGVVSSDGKTV TITFAADDSDNVVIHLKHGL EHHHHHH

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
spectral_peak_list

Data type	Count
13C chemical shifts	337
15N chemical shifts	87
1H chemical shifts	523

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	PtR41O	1

Entities:

Entity 1, PtR41O 87 residues - 9309.011 Da.

the 1st residue is initiating Methionine, 2nd to 79th residues are corresponding to residues 1288-1365 in the native protein, and 80th to 87th residues belong to purification tag.

1

MET

ASP

GLU

ASP

ALA

THR

ILE

THR

TYR

VAL

2

ASP

LYS

GLY

ALA

GLN

VAL

GLY

3

ASP

ILE

VAL

THR

VAL

THR

GLY

LYS

THR

ASP

4

ASP

SER

THR

TYR

THR

VAL

THR

ILE

PRO

5

ASP

GLY

TYR

GLU

TYR

VAL

GLY

THR

ASP

GLY

6

GLY

VAL

SER

ASP

GLY

LYS

THR

VAL

7

THR

ILE

THR

PHE

ALA

ASP

SER

ASP

8

ASN

VAL

ILE

HIS

LEU

LYS

HIS

GLY

LEU

9

GLU

HIS

Samples:

sample_4: PtR41O, [U-5% 13C; U-100% 15N], 0.66 mM; sodium chloride 66 mM; calcium chloride 3.3 mM; DTT 6.6 mM; MES 13.2 mM; NaN3 0.0132 % by volume; DSS 33 uM; Pf1 phage 13.25 mg/ml; H2O 83%; D2O 17%

sample_1: PtR41O, [U-100% 13C; U-100% 15N], 1.0 mM; sodium chloride 100 mM; calcium chloride 5 mM; DTT 10 mM; MES 20 mM; NaN3 0.02 % by volume; DSS 50 uM; H2O 90%; D2O 10%

sample_2: PtR41O, [U-5% 13C; U-100% 15N], 1.2 mM; sodium chloride 100 mM; calcium chloride 5 mM; DTT 10 mM; MES 20 mM; NaN3 0.02 % by volume; DSS 50 uM; H2O 90%; D2O 10%

sample_3: PtR41O, [U-5% 13C; U-100% 15N], 0.66 mM; sodium chloride 66 mM; calcium chloride 3.3 mM; DTT 6.6 mM; MES 13.2 mM; NaN3 0.0132 % by volume; DSS 33 uM; poly ethylene glycol 4 % by volume; H2O 83%; D2O 17%

sample_conditions_1: ionic strength: 117.5 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C CT-HSQC ali	sample_1	isotropic	sample_conditions_1
2D 1H-13C CT-HSQC aro	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HN(CA)CO	sample_1	isotropic	sample_conditions_1
GFT CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
GFT HNCACB	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D HCCH-COSY ali	sample_1	isotropic	sample_conditions_1
13C/15N-NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-13C CT-HSQC (methyl)	sample_2	isotropic	sample_conditions_1
2D J-modulation 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
2D J-modulation 1H-15N HSQC	sample_3	anisotropic	sample_conditions_1
2D J-modulation 1H-15N HSQC	sample_4	anisotropic	sample_conditions_1

Software:

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinemen,structure solution,geometry optimization

CYANA v3.0, Guntert, Mumenthaler and Wuthrich - refinement, structure solution

AutoStruct v2.2.1, Huang, Tejero, Powers and Montelione - structure solution

AutoAssign, Zimmerman, Moseley, Kulikowski and Montelione - chemical shift assignment

NMRPipe v2007.030.16.06, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

XEASY, Bartels et al. - data analysis

TOPSPIN, Bruker Biospin - collection

VNMRJ v2.1B, Varian - collection

Molmol, Koradi, Billeter and Wuthrich - refinement

CARA v1.8.4, Keller and Wuthrich - chemical shift assignment, data analysis, peak picking

TALOS+, Shen, Cornilescu, Delaglio and Bax - data analysis

PSVS v1.3, Bhattacharya and Montelione - validation

NMRDraw v3.0, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - data analysis

PROSA, Guntert - processing

NMR spectrometers:

Varian INOVA 750 MHz
Varian INOVA 500 MHz
Bruker Avance 600 MHz
Varian INOVA 600 MHz