BMRB Entry 18758

Name: Refined solution structure and dynamics of First Catalytic Cysteine Half-domain from mouse E1 enzyme
Published: 2013-09-16

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PDB ID: 2lzj
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR18758
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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:

Refined solution structure and dynamics of First Catalytic Cysteine Half-domain from mouse E1 enzyme

Deposition date:

2012-10-03

Original release date:

2013-09-16

Authors:

Jaremko, Mariusz; Jaremko, Lukasz; Nowakowski, Michal; Szczepanowski, Roman; Filipek, Renata; Wojciechowski, Marek; Bochtler, Matthias; Ejchart, Andrzej

Citation:

Citation: Jaremko, Mariusz; Jaremko, ukasz; Nowakowski, Micha; Wojciechowski, Marek; Szczepanowski, Roman; Panecka, Renata; Zhukov, Igor; Bochtler, Matthias; Ejchart, Andrzej. "NMR structural studies of the first catalytic half-domain of ubiquitin activating enzyme." J. Struct. Biol. 185, 69-78 (2014).
PubMed: 24211821

Assembly members:

Assembly members:
entity, polymer, 112 residues, 12195.902 Da.

Natural source:

Natural source: Common Name: Mouse Taxonomy ID: 10090 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Mus musculus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Saccharomyces cerevisiae Vector: pRS416 and pRS413

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity: EFGEEMVLTDSNGEQPLSAM VSMVTKDNPGVVTCLDEARH GFETGDFVSFSEVQGMIQLN GCQPMEIKVLGPYTFSICDT SNFSDYIRGGIVSQVKVPKK ISFKSLPASLVE

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
heteronucl_NOEs
- heteronuclear_noe_list_1
heteronucl_T1_relaxation
- heteronuclear_T1_list_1
heteronucl_T2_relaxation
- heteronuclear_T2_list_1
order_parameters
- order_parameter_list_1

Data type	Count
13C chemical shifts	469
15N chemical shifts	110
1H chemical shifts	769
heteronuclear NOE values	99
order parameters	71
T1 relaxation values	100
T2 relaxation values	99

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	First Catalytic Cysteine Half-domain	1

Entities:

Entity 1, First Catalytic Cysteine Half-domain 112 residues - 12195.902 Da.

1

GLU

PHE

GLY

GLU

MET

VAL

LEU

THR

ASP

2

SER

ASN

GLY

GLU

GLN

PRO

LEU

SER

ALA

MET

3

VAL

SER

MET

VAL

THR

LYS

ASP

ASN

PRO

GLY

4

VAL

THR

CYS

LEU

ASP

GLU

ALA

ARG

HIS

5

GLY

PHE

GLU

THR

GLY

ASP

PHE

VAL

SER

PHE

6

SER

GLU

VAL

GLN

GLY

MET

ILE

GLN

LEU

ASN

7

GLY

CYS

GLN

PRO

MET

GLU

ILE

LYS

VAL

LEU

8

GLY

PRO

TYR

THR

PHE

SER

ILE

CYS

ASP

THR

9

SER

ASN

PHE

SER

ASP

TYR

ILE

ARG

GLY

10

ILE

VAL

SER

GLN

VAL

LYS

VAL

PRO

LYS

11

ILE

SER

PHE

LYS

SER

LEU

PRO

ALA

SER

LEU

12

VAL

GLU

Samples:

sample_1: First Cysteine Catalytic Half-domain, [U-100% 13C; U-100% 15N], 1 mM; H2O 90 mM; D2O 10 mM

sample_2: First Cysteine Catalytic Half-domain, [U-100% 15N], 1 mM; H2O 90 mM; D2O 10 mM

sample_conditions_1: ionic strength: 50 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 50 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
2D 1H-13C HSQC aliphatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HNHA	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	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

Software:

X-PLOR NIH v2.26, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - peak picking

SPARKY, Goddard - chemical shift assignment

WhatIF, Vriend - refinement

NMR spectrometers:

Varian UnityPlus 500 MHz
Bruker Avance 700 MHz
Varian INOVA 400 MHz

PDB	2LZJ 2V31
DBJ	BAA01433 BAC40121 BAC40405 BAE25369 BAE42599
GB	AAH58630 AAI38201 AAI45985 EDL00743
REF	NP_001129557 NP_001263245 NP_001263246 NP_033483
SP	Q02053
AlphaFold	Q02053