BMRB Entry 11017

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PDB ID: 2rn7
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/BMR11017
MolProbity Validation Chart

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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR solution structure of TnpE protein from Shigella flexneri. Northeast Structural Genomics Target SfR125.

Deposition date:

2007-12-07

Original release date:

2008-03-24

Authors:

Ramelot, Theresa; Cort, John; Semesi, Anthony; Garcia, M; Yee, Adelinda; Arrowsmith, Cheryl; Kennedy, Michael

Citation:

Citation: Ramelot, Theresa; Cort, John; Semesi, Anthony; Garcia, M; Yee, Adelinda; Arrowsmith, Cheryl; Kennedy, Michael. "NMR solution structure of TnpE protein from Shigella flexneri. Northeast Structural Genomics Target SfR125." .

Assembly members:

Assembly members:
TnpE, polymer, 108 residues, 12666.427 Da.

Natural source:

Natural source: Common Name: Shigella flexneri Taxonomy ID: 623 Superkingdom: Bacteria Kingdom: not available Genus/species: Shigella flexneri

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: p15Tv lic

Entity Sequences (FASTA):

Entity Sequences (FASTA):
TnpE: MTKNTRFSPEVRQRAVRMVL ESQGEYDSQWATICSIAPKI GCTPETLRVWVRQHERDTGG DDGGLTTAERQRLKEPEREN RELRRSNDILRLASAYFAKA EFDRLWKK

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
spectral_peak_list

Data type	Count
13C chemical shifts	386
15N chemical shifts	94
1H chemical shifts	606

Time Domain Data

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	TnpE	1

Entities:

Entity 1, TnpE 108 residues - 12666.427 Da.

1

MET

THR

LYS

ASN

THR

ARG

PHE

SER

PRO

GLU

2

VAL

ARG

GLN

ARG

ALA

VAL

ARG

MET

VAL

LEU

3

GLU

SER

GLN

GLY

GLU

TYR

ASP

SER

GLN

TRP

4

ALA

THR

ILE

CYS

SER

ILE

ALA

PRO

LYS

ILE

5

GLY

CYS

THR

PRO

GLU

THR

LEU

ARG

VAL

TRP

6

VAL

ARG

GLN

HIS

GLU

ARG

ASP

THR

GLY

7

ASP

GLY

LEU

THR

ALA

GLU

ARG

8

GLN

ARG

LEU

LYS

GLU

PRO

GLU

ARG

GLU

ASN

9

ARG

GLU

LEU

ARG

SER

ASN

ASP

ILE

LEU

10

ARG

LEU

ALA

SER

ALA

TYR

PHE

ALA

LYS

ALA

11

GLU

PHE

ASP

ARG

LEU

TRP

LYS

Samples:

CN_sample: TnpE, [U-100% 13C; U-100% 15N], 1 ± 0.1 mM; TRIS 10 ± 1 mM; sodium chloride 500 ± 50 mM; DTT 10 ± 1 mM; Zn+2 10 ± 1 uM; sodium azide 0.01 ± 0.01 %; benzamidine 1 ± 0.1 mM; H2O 90%; D2O 10%

NC7_sample: TnpE, [U-7% 13C; U-100% 15N], 1 ± 0.1 mM; TRIS 10 ± 1 mM; sodium chloride 500 ± 50 mM; DTT 10 ± 1 mM; Zn+2 10 ± 1 uM; sodium azide 0.01 ± 0.01 %; benzamidine 1 ± 0.1 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.5 M; pH: 7.7; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	CN_sample	isotropic	sample_conditions_1
2D 1H-13C HSQC (aliph)	CN_sample	isotropic	sample_conditions_1
3D HNCACB	CN_sample	isotropic	sample_conditions_1
3D CBCA(CO)NH	CN_sample	isotropic	sample_conditions_1
3D HNCO	CN_sample	isotropic	sample_conditions_1
3D HBHA(CO)NH	CN_sample	isotropic	sample_conditions_1
3D C(CO)NH	CN_sample	isotropic	sample_conditions_1
3D HCCH-TOCSY	CN_sample	isotropic	sample_conditions_1
3D (H)CCH-TOCSY	CN_sample	isotropic	sample_conditions_1
2D 1H-15N HSQC	CN_sample	isotropic	sample_conditions_1
3D 1H-15N NOESY	CN_sample	isotropic	sample_conditions_1
3D 1H-13C NOESY aliph	CN_sample	isotropic	sample_conditions_1
3D 1H-13C NOESY arom	CN_sample	isotropic	sample_conditions_1
3D HCCH-COSY	CN_sample	isotropic	sample_conditions_1
2D 1H-13C HSQC	CN_sample	isotropic	sample_conditions_1
2D 1H-15N HSQC	NC7_sample	isotropic	sample_conditions_1
2D 1H-13C HSQC	NC7_sample	isotropic	sample_conditions_1
2D 1H-13C HSQC (arom ct)	CN_sample	isotropic	sample_conditions_1

Software:

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

VNMR v6.1C, Varian - collection

AutoStruct v2.1.1, Huang, Tejero, Powers and Montelione - data analysis

X-PLOR NIH v2.15.0, Schwieters, Kuszewski, Tjandra and Clore - structure solution

CNS v1.1, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

SPARKY v3.1, Goddard - data analysis

NMR spectrometers:

Varian INOVA 600 MHz
Varian INOVA 750 MHz

SWS	Q99Q67
UNP	Q99Q67_SHIFL
PDB	2RN7
DBJ	BAI57971 BAN82908 BAN82936
EMBL	CAR16451 CAR16627 CAR18772 CAR19494 CAR19546
GB	AAC44574 AAD44738 AAF09023 AAK18356 AAK18368
REF	NP_085200 NP_085212 NP_085224 NP_085240 NP_085247
AlphaFold	Q99Q67