BMRB Entry 16929

Name: NMR structure and calcium-binding properties of the tellurite resistance protein TerD from Klebsiella pneumoniae
Published: 2010-12-02

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PDB ID: 2kxv
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16929
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR structure and calcium-binding properties of the tellurite resistance protein TerD from Klebsiella pneumoniae

Deposition date:

2010-05-14

Original release date:

2010-12-02

Authors:

Pan, Yun-Ru; Lou, Yuan-Chou; Rizo, Josep; Chen, Chinpan

Citation:

Citation: Pan, Yun-Ru; Lou, Yuan-Chao; Seven, Alpay; Rizo, Josep; Chen, Chinpan. "NMR Structure and Calcium-Binding Properties of the Tellurite Resistance Protein TerD from Klebsiella pneumoniae." J. Mol. Biol. 405, 1188-1201 (2011).
PubMed: 21112337

Assembly members:

Assembly members:
TerD, polymer, 200 residues, 21558.7 Da.
CA, non-polymer, 40.078 Da.

Natural source:

Natural source: Common Name: K. pneumoniae Taxonomy ID: 573 Superkingdom: Bacteria Kingdom: not available Genus/species: Klebsiella pneumoniae

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: BL 21 DE3

Entity Sequences (FASTA):

Entity Sequences (FASTA):
TerD: MSVSLSKGGNVSLSKTAPSM KNVLVGLGWDARSTDGQDFD LDASAFLLAANGKVRGDADF IFYNNLKSADGSVTHTGDNR TGEGDGDDESLKIKLDAVPG DVDKIIFVVTIHDAQARRQS FGQVSGAFIRLVNDDNQTEV ARYDLTEDASTETAMLFGEL YRHNGEWKFRAVGQGYAGGL ASVCAQYGINASLEHHHHHH

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	806
15N chemical shifts	203
1H chemical shifts	1209

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	TerD	1
2	CA	2

Entities:

Entity 1, TerD 200 residues - 21558.7 Da.

1	MET	SER	VAL	SER	LEU	SER	LYS	GLY	GLY	ASN
2	VAL	SER	LEU	SER	LYS	THR	ALA	PRO	SER	MET
3	LYS	ASN	VAL	LEU	VAL	GLY	LEU	GLY	TRP	ASP
4	ALA	ARG	SER	THR	ASP	GLY	GLN	ASP	PHE	ASP
5	LEU	ASP	ALA	SER	ALA	PHE	LEU	LEU	ALA	ALA
6	ASN	GLY	LYS	VAL	ARG	GLY	ASP	ALA	ASP	PHE
7	ILE	PHE	TYR	ASN	ASN	LEU	LYS	SER	ALA	ASP
8	GLY	SER	VAL	THR	HIS	THR	GLY	ASP	ASN	ARG
9	THR	GLY	GLU	GLY	ASP	GLY	ASP	ASP	GLU	SER
10	LEU	LYS	ILE	LYS	LEU	ASP	ALA	VAL	PRO	GLY
11	ASP	VAL	ASP	LYS	ILE	ILE	PHE	VAL	VAL	THR
12	ILE	HIS	ASP	ALA	GLN	ALA	ARG	ARG	GLN	SER
13	PHE	GLY	GLN	VAL	SER	GLY	ALA	PHE	ILE	ARG
14	LEU	VAL	ASN	ASP	ASP	ASN	GLN	THR	GLU	VAL
15	ALA	ARG	TYR	ASP	LEU	THR	GLU	ASP	ALA	SER
16	THR	GLU	THR	ALA	MET	LEU	PHE	GLY	GLU	LEU
17	TYR	ARG	HIS	ASN	GLY	GLU	TRP	LYS	PHE	ARG
18	ALA	VAL	GLY	GLN	GLY	TYR	ALA	GLY	GLY	LEU
19	ALA	SER	VAL	CYS	ALA	GLN	TYR	GLY	ILE	ASN
20	ALA	SER	LEU	GLU	HIS	HIS	HIS	HIS	HIS	HIS

Entity 2, CA - Ca - 40.078 Da.

1

CA

Samples:

KP-TerD: potassium phosphate 20 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.02 M; pH: 7; pressure: 1 atm; temperature: 310 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	KP-TerD	isotropic	sample_conditions_1
2D 1H-13C HSQC	KP-TerD	isotropic	sample_conditions_1
3D CBCA(CO)NH	KP-TerD	isotropic	sample_conditions_1
3D HNCACB	KP-TerD	isotropic	sample_conditions_1
3D HNCO	KP-TerD	isotropic	sample_conditions_1
3D HN(CO)CA	KP-TerD	isotropic	sample_conditions_1
3D C(CO)NH	KP-TerD	isotropic	sample_conditions_1
3D 1H-15N NOESY	KP-TerD	isotropic	sample_conditions_1
3D 1H-13C NOESY	KP-TerD	isotropic	sample_conditions_1
3D HCCH-TOCSY	KP-TerD	isotropic	sample_conditions_1
3D HBHA(CO)NH	KP-TerD	isotropic	sample_conditions_1
3D HNHA	KP-TerD	isotropic	sample_conditions_1
2D 1H-1H NOESY	KP-TerD	isotropic	sample_conditions_1
2D CACO (ipap)	KP-TerD	isotropic	sample_conditions_1

Software:

AURELIA v3.1.6, Linge, O'Donoghue and Nilges - data analysis

xwinnmr v3.5, Bruker Biospin - processing

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure solution

VNMR v5.0, Johnson, One Moon Scientific - chemical shift assignment

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMR spectrometers:

Bruker Avance 800 MHz

PDB	2KXT 2KXV
DBJ	BAH66157
EMBL	CAJ86458 CDI26595 CDM79667 CEO83282 CEP33510
GB	AAA98292 AAR07677 ABF67755 ABU77054 ACI11978
PRF	2009362B
REF	NP_943327 WP_000116676 WP_000116677 WP_004026609 WP_004181727
SP	P18781
AlphaFold	P18781

1	MET	SER	VAL	SER	LEU	SER	LYS	GLY	GLY	ASN
2	VAL	SER	LEU	SER	LYS	THR	ALA	PRO	SER	MET
3	LYS	ASN	VAL	LEU	VAL	GLY	LEU	GLY	TRP	ASP
4	ALA	ARG	SER	THR	ASP	GLY	GLN	ASP	PHE	ASP
5	LEU	ASP	ALA	SER	ALA	PHE	LEU	LEU	ALA	ALA
6	ASN	GLY	LYS	VAL	ARG	GLY	ASP	ALA	ASP	PHE
7	ILE	PHE	TYR	ASN	ASN	LEU	LYS	SER	ALA	ASP
8	GLY	SER	VAL	THR	HIS	THR	GLY	ASP	ASN	ARG
9	THR	GLY	GLU	GLY	ASP	GLY	ASP	ASP	GLU	SER
10	LEU	LYS	ILE	LYS	LEU	ASP	ALA	VAL	PRO	GLY
11	ASP	VAL	ASP	LYS	ILE	ILE	PHE	VAL	VAL	THR
12	ILE	HIS	ASP	ALA	GLN	ALA	ARG	ARG	GLN	SER
13	PHE	GLY	GLN	VAL	SER	GLY	ALA	PHE	ILE	ARG
14	LEU	VAL	ASN	ASP	ASP	ASN	GLN	THR	GLU	VAL
15	ALA	ARG	TYR	ASP	LEU	THR	GLU	ASP	ALA	SER
16	THR	GLU	THR	ALA	MET	LEU	PHE	GLY	GLU	LEU
17	TYR	ARG	HIS	ASN	GLY	GLU	TRP	LYS	PHE	ARG
18	ALA	VAL	GLY	GLN	GLY	TYR	ALA	GLY	GLY	LEU
19	ALA	SER	VAL	CYS	ALA	GLN	TYR	GLY	ILE	ASN
20	ALA	SER	LEU	GLU	HIS	HIS	HIS	HIS	HIS	HIS

1	MET	SER	VAL	SER	LEU	SER	LYS	GLY	GLY	ASN
2	VAL	SER	LEU	SER	LYS	THR	ALA	PRO	SER	MET
3	LYS	ASN	VAL	LEU	VAL	GLY	LEU	GLY	TRP	ASP
4	ALA	ARG	SER	THR	ASP	GLY	GLN	ASP	PHE	ASP
5	LEU	ASP	ALA	SER	ALA	PHE	LEU	LEU	ALA	ALA
6	ASN	GLY	LYS	VAL	ARG	GLY	ASP	ALA	ASP	PHE
7	ILE	PHE	TYR	ASN	ASN	LEU	LYS	SER	ALA	ASP
8	GLY	SER	VAL	THR	HIS	THR	GLY	ASP	ASN	ARG
9	THR	GLY	GLU	GLY	ASP	GLY	ASP	ASP	GLU	SER
10	LEU	LYS	ILE	LYS	LEU	ASP	ALA	VAL	PRO	GLY
11	ASP	VAL	ASP	LYS	ILE	ILE	PHE	VAL	VAL	THR
12	ILE	HIS	ASP	ALA	GLN	ALA	ARG	ARG	GLN	SER
13	PHE	GLY	GLN	VAL	SER	GLY	ALA	PHE	ILE	ARG
14	LEU	VAL	ASN	ASP	ASP	ASN	GLN	THR	GLU	VAL
15	ALA	ARG	TYR	ASP	LEU	THR	GLU	ASP	ALA	SER
16	THR	GLU	THR	ALA	MET	LEU	PHE	GLY	GLU	LEU
17	TYR	ARG	HIS	ASN	GLY	GLU	TRP	LYS	PHE	ARG
18	ALA	VAL	GLY	GLN	GLY	TYR	ALA	GLY	GLY	LEU
19	ALA	SER	VAL	CYS	ALA	GLN	TYR	GLY	ILE	ASN
20	ALA	SER	LEU	GLU	HIS	HIS	HIS	HIS	HIS	HIS