BMRB Entry 6448

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PDB ID: 1xhs
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR6448
MolProbity Validation Chart

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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 structure of the hypothetical protein ytfP from Escherichia coli. Northeast Structural Genomics target ER111.

Deposition date:

2004-12-28

Original release date:

2005-06-12

Authors:

Aramini, J.; Huang, Y.; Swapna, G.; Paranji, R.; Xiao, R.; Shastry, R.; Acton, T.; Cort, J.; Kennedy, M.; Montelione, G.

Citation:

Citation: Aramini, J.; Swapna, G.; Huang, Y.; Rajan, P.; Xiao, R.; Shastry, R.; Acton, T.; Cort, J.; Kennedy, M.; Montelione, G.. "1H, 13C, and 15N Resonance Assignments for Escherichia coli ytfP, a Member of the Broadly Conserved UPF0131 Protein Domain Family" J. Biomol. NMR 33, 197-197 (2005).

Assembly members:

Assembly members:
Hypothetical UPF0131 protein ytfP, polymer, 121 residues, Formula weight is not available

Natural source:

Natural source: Common Name: E. coli Taxonomy ID: 562 Superkingdom: Eubacteria Kingdom: not available Genus/species: Escherichia coli

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: PET21

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Hypothetical UPF0131 protein ytfP: MRIFVYGSLRHKQGNSHWMT NAQLLGDFSIDNYQLYSLGH YPGAVPGNGTVHGEVYRIDN ATLAELDALRTRGGEYARQL IQTPYGSAWMYVYQRPVDGL KLIESGDWLDRDKLEHHHHH H

Data sets:

assigned_chemical_shifts
- chemical_shift_set_1
coupling_constants
- coupling_constants_set_1

Data type	Count
1H chemical shifts	797
13C chemical shifts	508
15N chemical shifts	127
coupling constants	61

Time Domain Data

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Hypothetical UPF0131 protein ytfP	1

Entities:

Entity 1, Hypothetical UPF0131 protein ytfP 121 residues - Formula weight is not available

1

MET

ARG

ILE

PHE

VAL

TYR

GLY

SER

LEU

ARG

2

HIS

LYS

GLN

GLY

ASN

SER

HIS

TRP

MET

THR

3

ASN

ALA

GLN

LEU

GLY

ASP

PHE

SER

ILE

4

ASP

ASN

TYR

GLN

LEU

TYR

SER

LEU

GLY

HIS

5

TYR

PRO

GLY

ALA

VAL

PRO

GLY

ASN

GLY

THR

6

VAL

HIS

GLY

GLU

VAL

TYR

ARG

ILE

ASP

ASN

7

ALA

THR

LEU

ALA

GLU

LEU

ASP

ALA

LEU

ARG

8

THR

ARG

GLY

GLU

TYR

ALA

ARG

GLN

LEU

9

ILE

GLN

THR

PRO

TYR

GLY

SER

ALA

TRP

MET

10

TYR

VAL

TYR

GLN

ARG

PRO

VAL

ASP

GLY

LEU

11

LYS

LEU

ILE

GLU

SER

GLY

ASP

TRP

LEU

ASP

12

ARG

ASP

LYS

LEU

GLU

HIS

13

HIS

Samples:

sample_1: Hypothetical UPF0131 protein ytfP, [U-13C; U-15N], 1.3 mM; NH4OAC 20 mM; CACL2 5 mM; NaCL 0.1 M; DTT 10 mM; NAN3 0.02%; D2O 5%; H2O 95%

sample_2: Hypothetical UPF0131 protein ytfP, [U-13C; U-15N], 1.3 mM; NH4OAC 20 mM; CACL2 5 mM; NaCL 0.1 M; DTT 10 mM; NAN3 0.02%; D2O 100%

sample_3: Hypothetical UPF0131 protein ytfP, [U-5% 13C; U-15N], 1.1 mM; NH4OAC 20 mM; CACL2 5 mM; NaCL 0.1 M; DTT 10 mM; NAN3 0.02%; D2O 5%; H2O 95%

sample_cond_1: pH: 5.5; temperature: 293 K; ionic strength: 100 mM; pressure: 1 atm

Experiments:

Name	Sample	Sample state	Sample conditions
3D 15N-SEPARATED NOESY	not available	not available	not available
3D 13C-SEPARATED NOESY (aliph)	not available	not available	not available
4D 13C-SEPARATED NOESY	not available	not available	not available
HNHA	not available	not available	not available
HIGH RESOLUTION CH-HSQC	not available	not available	not available
3D HNCO	not available	not available	not available
HCCH TOCSY	not available	not available	not available
HCCH COSY	not available	not available	not available
3D 13C-SEPARATED NOESY (arom)	not available	not available	not available
3D HNCOCACB	not available	not available	not available
3D HNCACB	not available	not available	not available
3D HNCOCA	not available	not available	not available
3D HNCA	not available	not available	not available
3D HNCACO	not available	not available	not available
HCCONH	not available	not available	not available
CCONH	not available	not available	not available
HACANH	not available	not available	not available
HACACONH	not available	not available	not available
HBCBcgcdHD	not available	not available	not available

Software:

AUTOSTRUCTURE 2.1.0, XPLOR-NIH 2.0.6, CNS v1.1 - refinement

VNMR v6.1C - structure solution

PSVS v1.0 - structure solution

NMRPIPE v2.3 - structure solution

SPARKY v3.91 - structure solution

AUTOASSIGN v1.14 - structure solution

HYPER v3.2 - structure solution

PDBSTAT v3.27 - structure solution

NMR spectrometers:

Varian Inova 800 MHz
Varian Inova 750 MHz
Varian Inova 600 MHz
Varian Inova 500 MHz

PDB	1XHS
DBJ	BAB38623 BAE78223 BAG80052 BAI28527 BAI33701
EMBL	CAP78743 CAQ34574 CAQ91721 CAR01197 CAR05964
GB	AAA97119 AAC77179 AAG59420 AAN45683 AAN83741
REF	NP_290854 NP_313227 NP_418643 NP_709976 NP_757167
SP	P0AE48 P0AE49 P0AE50 P0AE51
AlphaFold	P0AE48 P0AE49 P0AE50 P0AE51