BMRB Entry 17799

Name: NMR structure of the protein YP_001302112.1 from Parabacteroides distasonis
Published: 2011-08-25

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PDB ID: 2lg7
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR17799
MolProbity Validation Chart

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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR structure of the protein YP_001302112.1 from Parabacteroides distasonis

Deposition date:

2011-07-22

Original release date:

2011-08-25

Authors:

Serrano, Pedro; Mohanty, Biswaranjan; Geralt, Michael; Wuthrich, Kurt

Citation:

Citation: Serrano, Pedro; Mohanty, Biswaranjan; Geralt, Michael; Wuthrich, Kurt. "NMR structure of the protein YP_001302112.1 from Parabacteroides distasonis" .

Assembly members:

Assembly members:
entity, polymer, 200 residues, 13807.372 Da.

Natural source:

Natural source: Common Name: Parabacteroides distasonis Taxonomy ID: 823 Superkingdom: Bacteria Kingdom: Parabacteroides Genus/species: Parabacteroides distasonis

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity: MRKYLYLSAVCVCMALCFVG CSKDDDEPGGKGAMYEVTIE QSGDFRSFIKSVVVVANGTQ LKDGATGESLASPVILSDEE LAVEKVTLSTTGKAIEFAVS GGVVDGEDGVVNEPMQWVVT VYKNGKEIEKKSLVFRDGKE ISTDDLNLYYNVVDGEDGVV NEPMQWVVTVYKNGKEIEKK SLVFRDGKEISTDDLNLYYN

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	488
15N chemical shifts	124
1H chemical shifts	784

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	YP_001302112	1

Entities:

Entity 1, YP_001302112 200 residues - 13807.372 Da.

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

Samples:

sample_1: YP_001302112, [U-98% 13C; U-98% 15N], 1.2 mM; sodium phosphate 20 mM; sodium chloride 25 mM; sodium azide 5 mM; H2O 95%; D2O 5%

sample_conditions_1: ionic strength: 0.18 M; pH: 6.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
5D APSY CBCACONH	sample_1	isotropic	sample_conditions_1
4D APSY HACANH	sample_1	isotropic	sample_conditions_1
5D APSY HACACONH	sample_1	isotropic	sample_conditions_1

Software:

CYANA, G ntert P. - refinement, structure solution

TOPSPIN, Bruker Biospin - collection, data analysis, processing

OPAL, Luginbuhl, Guntert, Billeter and Wuthrich - refinement

UNIO, Unio Herrmann Wuthrich - chemical shift assignment, peak picking

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 800 MHz

BMRB	17806
PDB	2LG7 2LGE
EMBL	CUP04873 CUP86285 CUQ25107
GB	AAO45318 ABR42490 EFG18115 EFK63750 EIY16653
REF	NP_818973 WP_005842168 WP_007659490 WP_032583709

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

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