BMRB Entry 25850

Name: Solution NMR Structure of Designed Protein DA05, Northeast Structural Genomics Consortium (NESG) Target OR626
Published: 2016-01-19

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PDB ID: 2n8i
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25850
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 Designed Protein DA05, Northeast Structural Genomics Consortium (NESG) Target OR626

Deposition date:

2015-10-19

Original release date:

2016-01-19

Authors:

Xu, Xianzhong; Eletsky, Alexander; Federizon, Jasmin; Jacobs, Tim; Kuhlman, Brian; Szyperski, Thomas

Citation:

Citation: Jacobs, Tim; Xu, Xianzhong; Eletsky, Alexander; Federizon, Jasmin; Szyperski, Thomas; Kuhlman, Brian. "Design of Structurally Unique Proteins Using Strategies Inspired by Evolution" .

Assembly members:

Assembly members:
DA05, polymer, 200 residues, 22279.326 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: not available Superkingdom: not available Kingdom: not available Genus/species: not available not available

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pQE-HT

Entity Sequences (FASTA):

Entity Sequences (FASTA):
DA05: GGSPDENIAKFEKAYKKAEE LNQGELMGRALYNIGLEKNK MGKVKEAIEYFLRAKKVFDA EHDTDGARRAAKSLSEAYQK VEGSGDKGKIFQKEGESILE GGSPDENIAKFEKAYKKAEE LNQGELMGRALYNIGLEKNK MGKVKEAIEYFLRAKKVFDA EHDTDGARRAAKSLSEAYQK VEGSGDKGKIFQKEGESILE

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
spectral_peak_list

Data type	Count
13C chemical shifts	440
15N chemical shifts	104
1H chemical shifts	701

Time Domain Data

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	DA05	1

Entities:

Entity 1, DA05 200 residues - 22279.326 Da.

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

Samples:

NC: DA05, [U-13C; U-15N], 600 uM; sodium phosphate 25 mM; sodium chloride 50 mM; sodium azide 0.02%; PMSF 0.5 mM; DSS 50 uM

NC5: DA05, [U-5% 13C; U-15N], 200 uM; sodium phosphate 25 mM; sodium chloride 50 mM; sodium azide 0.02%; PMSF 0.5 mM; DSS 50 uM

sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	NC	isotropic	sample_conditions_1
2D CT 1H-13C HSQC aliphatic	NC	isotropic	sample_conditions_1
2D CT 1H-13C HSQC aromatic	NC	isotropic	sample_conditions_1
3D 15N/13C-edited 1H-1H NOESY	NC	isotropic	sample_conditions_1
(4,3)D GFT HCCH-COSY aliphatic	NC	isotropic	sample_conditions_1
(4,3)D GFT HCCH-COSY aromatic	NC	isotropic	sample_conditions_1
(4,3)D GFT HNNCACBCA	NC	isotropic	sample_conditions_1
3D (H)CCH-TOCSY	NC	isotropic	sample_conditions_1
3D HNCO	NC	isotropic	sample_conditions_1
3D HN(CA)CO	NC	isotropic	sample_conditions_1
(4,3)D GFT CABCA(CO)NHN	NC	isotropic	sample_conditions_1
2D CT 1H-13C HSQC aliphatic 28 ms	NC5	isotropic	sample_conditions_1
2D CT 1H-13C HSQC aliphatic 42 ms	NC5	isotropic	sample_conditions_1
2D CT 1H-13C HSQC aliphatic 56 ms	NC5	isotropic	sample_conditions_1

Software:

PROSA v6.4, Guntert - processing

AS-DP v1.0, Huang, Tejero, Powers and Montelione - structure solution

CNS v1.3, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

CARA v1.8.4, Keller and Wuthrich - chemical shift assignment, data analysis, peak picking

CYANA v3.0, Guntert, Mumenthaler and Wuthrich - structure solution

XEASY v1.3.13, Bartels et al. - data analysis

VNMRJ v4.0, Varian - collection

TALOS-N, Cornilescu, Delaglio and Bax - geometry optimization

PSVS v1.5, Bhattacharya and Montelione - structure validation

AutoAssign v2.3.0, Zimmerman, Moseley, Kulikowski and Montelione - chemical shift assignment

NMR spectrometers:

Varian INOVA 750 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks

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

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

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