BMRB Entry 19811

Name: NMR solution structure of a computational designed protein based on template of human erythrocytic ubiquitin
Published: 2014-10-27

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PDB ID: 2mlb
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19811
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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:

NMR solution structure of a computational designed protein based on template of human erythrocytic ubiquitin

Deposition date:

2014-02-21

Original release date:

2014-10-27

Authors:

Xiong, Peng; Wang, Meng; Zhang, Jiahai; Chen, Quan; Liu, Haiyan

Citation:

Citation: Xiong, Peng; Wang, Meng; Zhou, Xiaoqun; Zhang, Tongchuan; Zhang, Jiahai; Chen, Quan; Liu, Haiyan. "A comprehensive statistical energy function for protein design" Nat. Methods ., .-..

Assembly members:

Assembly members:
redesigned_ubiquitin, polymer, 79 residues, 8559.913 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: pET22b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
redesigned_ubiquitin: MDTINITLPDGKTLTLTVTP EFTVKELAEEIARRLGLSPE DIKLTHNGKTLDPSLTLAEY GITPGSTITLEIKKKGGLE

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	264
15N chemical shifts	76
1H chemical shifts	561

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	redesigned ubiquitin	1

Entities:

Entity 1, redesigned ubiquitin 79 residues - 8559.913 Da.

1

MET

ASP

THR

ILE

ASN

ILE

THR

LEU

PRO

ASP

2

GLY

LYS

THR

LEU

THR

LEU

THR

VAL

THR

PRO

3

GLU

PHE

THR

VAL

LYS

GLU

LEU

ALA

GLU

4

ILE

ALA

ARG

LEU

GLY

LEU

SER

PRO

GLU

5

ASP

ILE

LYS

LEU

THR

HIS

ASN

GLY

LYS

THR

6

LEU

ASP

PRO

SER

LEU

THR

LEU

ALA

GLU

TYR

7

GLY

ILE

THR

PRO

GLY

SER

THR

ILE

THR

LEU

8

GLU

ILE

LYS

GLY

LEU

GLU

Samples:

sample_1: redesigned ubiquitin, [U-100% 15N], 0.5 – 1 mM; phosphate buffer 25 mM; sodium chloride 100 mM; EDTA 2 mM; D2O, [U-100% 2H], 10%; H2O 90%

sample_2: redesigned ubiquitin, [U-100% 13C], 0.5 – 1 mM; phosphate buffer 25 mM; sodium chloride 100 mM; EDTA 2 mM; D2O, [U-100% 2H], 100%

sample_conditions_1: ionic strength: 125 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_2	isotropic	sample_conditions_1
3D HCCH-COSY	sample_2	isotropic	sample_conditions_1

Software:

CNS v1.3, Brunger, Adams, Clore, Gros, Nilges and Read - geometry optimization, refinement, structure solution

NMR spectrometers:

Bruker DMX 600 MHz