BMRB Entry 7274

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PDB ID: 2hh8
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR7274
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 NMR structure of the YdfO protein from Escherichia coli. Northeast Structural Genomics target ER251

Deposition date:

2006-08-24

Original release date:

2007-02-01

Authors:

Rossi, P.; Cort, J.; Ho, C.; Janjua, H.; Cunningham, K.; Ma, L.-C.; Xiao, R.; Liu, J.; Baran, M.; Swapna, G.; Acton, T.; Rost, B.; Kennedy, M.; Montelione, G.

Citation:

Citation: Rossi, P.; Cort, J.; Ho, C.; Janjua, H.; Cunningham, K.; Ma, L.-C.; Xiao, R.; Liu, J.; Baran, M.; Swapna, G.; Acton, T.; Rost, B.; Kennedy, M.; Montelione, G.. "Solution NMR structure of the YdfO protein from Escherichia coli. Northeast Structural Genomics target ER251" .

Assembly members:

Assembly members:
Hypothetical protein YdfO, polymer, 149 residues, Formula weight is not available

Natural source:

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

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Hypothetical protein YdfO: MEGLSMDQVVIFKQIFDKVR NDLNYQWFYSELKRHNVSHY IYYLATENVHIVLKNDNTVL LKGLKNIVSVKFSKDRHLIE TTSNKLKSREITFQEYRRNL AKAGVFRWVTNIHEQKRYYY TFDNSLLFTESIQKTTQIFP RLEHHHHHH

Data sets:

assigned_chemical_shifts
- chemical_shift_set_1

Data type	Count
13C chemical shifts	680
15N chemical shifts	168
1H chemical shifts	1013

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Hypothetical protein YdfO	1

Entities:

Entity 1, Hypothetical protein YdfO 149 residues - Formula weight is not available

1

MET

GLU

GLY

LEU

SER

MET

ASP

GLN

VAL

2

ILE

PHE

LYS

GLN

ILE

PHE

ASP

LYS

VAL

ARG

3

ASN

ASP

LEU

ASN

TYR

GLN

TRP

PHE

TYR

SER

4

GLU

LEU

LYS

ARG

HIS

ASN

VAL

SER

HIS

TYR

5

ILE

TYR

LEU

ALA

THR

GLU

ASN

VAL

HIS

6

ILE

VAL

LEU

LYS

ASN

ASP

ASN

THR

VAL

LEU

7

LEU

LYS

GLY

LEU

LYS

ASN

ILE

VAL

SER

VAL

8

LYS

PHE

SER

LYS

ASP

ARG

HIS

LEU

ILE

GLU

9

THR

SER

ASN

LYS

LEU

LYS

SER

ARG

GLU

10

ILE

THR

PHE

GLN

GLU

TYR

ARG

ASN

LEU

11

ALA

LYS

ALA

GLY

VAL

PHE

ARG

TRP

VAL

THR

12

ASN

ILE

HIS

GLU

GLN

LYS

ARG

TYR

13

THR

PHE

ASP

ASN

SER

LEU

PHE

THR

GLU

14

SER

ILE

GLN

LYS

THR

GLN

ILE

PHE

PRO

15

ARG

LEU

GLU

HIS

Samples:

sample_1: Hypothetical protein YdfO, [U-13C; U-15N], 0.69 mM; NaN3 0.02%; DTT 10 mM; CaCl2 5 mM; NaCl 100 mM; ammonium acetate 20 mM; D2O 5%; H2O 95%

sample_2: Hypothetical protein YdfO, [U-5% 13C; U-15N], 0.74 mM; NaN3 0.02%; DTT 10 mM; CaCl2 5 mM; NaCl 100 mM; ammonium acetate 20 mM; D2O 5%; H2O 95%

sample_3: Hypothetical protein YdfO, [U-13C; U-15N], 0.69 mM; NaN3 0.02%; DTT 10 mM; CaCl2 5 mM; NaCl 100 mM; ammonium acetate 20 mM; D2O 99.9%

sample_cond_1: ionic strength: 0.1 M; pH: 4.5; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 13C-separated NOESY	not available	not available	not available
3D 15N-separated NOESY	not available	not available	not available
HcCH-TOCSY	not available	not available	not available
HcCH-COSY	not available	not available	not available
CccoNH-TOCSY	not available	not available	not available
3D-HNCACB	not available	not available	not available
HNcoCACB	not available	not available	not available
HBHAcoNH	not available	not available	not available
HNCO	not available	not available	not available
13C HSQC noct Stereospecific VL Me assign.	not available	not available	not available
Het-NOE	not available	not available	not available
T1/T1rho	not available	not available	not available

Software:

VNMR v6.1C - collection

xwinnmr v3.5 - collection

DYANA v1.2 - structure solution

X-PLOR v2.11.2 - refinement

NMRPipe v2005 - processing

SPARKY v3.11 - data analysis

AutoAssign v2.2.1 - data analysis

AutoStruct v2.1.1 - structure solution

HYPER v2.1 - structure solution

PDBStat v4.1 - data analysis

PSVS v1.3 - refinement

CNS v1.1 - refinement

Procheck NMR v3.51 - refinement

MolProbity v3.01 - refinement

NMR spectrometers:

Varian INOVA 600 MHz

PDB	2HH8
DBJ	BAE76466 BAJ43349
EMBL	CAQ98449 CAR17640 CBG34523 CDJ71949 CDK69631
GB	AAC74622 AAN79909 ACA77728 ACB02759 ACR65380
REF	NP_416067 NP_753349 WP_000373089 WP_000373090 WP_000398761
SP	P76156
AlphaFold	P76156