BMRB Entry 18642

Name: Protein structure
Published: 2013-06-10

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PDB ID: 2lwr
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR18642
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:

Protein structure

Deposition date:

2012-08-06

Original release date:

2013-06-10

Authors:

Mercier, Pascal; Spratt, Donald; Manczyk, Noah; Shaw, Gary

Citation:

Citation: Spratt, Donald; Julio Martinez-Torres, R.; Noh, Yeong; Mercier, Pascal; Manczyk, Noah; Barber, Kathryn; Aguirre, Jacob; Burchell, Lynn; Purkiss, Andrew; Walden, Helen; Shaw, Gary. "A molecular explanation for the recessive nature of parkin-linked Parkinson's disease." Nat. Commun. 4, 1983-1983 (2013).
PubMed: 23770917

Assembly members:

Assembly members:
Protein, polymer, 68 residues, 7669.769 Da.
ZINC ION, non-polymer, 65.409 Da.

Natural source:

Natural source: Common Name: Fruit fly Taxonomy ID: 7227 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Drosophila melanogaster

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pGEX-6P-2

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Protein: GSAEARWDEASNVTIKVSTK PCPKCRTPTERDGGCMHMVC TRAGCGFEWCWVCQTEWTRD CMGAHWFG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	256
15N chemical shifts	63
1H chemical shifts	388

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Protein	1
2	ZINC ION_1	2
3	ZINC ION_2	2

Entities:

Entity 1, Protein 68 residues - 7669.769 Da.

N-terminal GS sequence results from the cleavage site

1

GLY

SER

ALA

GLU

ALA

ARG

TRP

ASP

GLU

ALA

2

SER

ASN

VAL

THR

ILE

LYS

VAL

SER

THR

LYS

3

PRO

CYS

PRO

LYS

CYS

ARG

THR

PRO

THR

GLU

4

ARG

ASP

GLY

CYS

MET

HIS

MET

VAL

CYS

5

THR

ARG

ALA

GLY

CYS

GLY

PHE

GLU

TRP

CYS

6

TRP

VAL

CYS

GLN

THR

GLU

TRP

THR

ARG

ASP

7

CYS

MET

GLY

ALA

HIS

TRP

PHE

GLY

Entity 2, ZINC ION_1 - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: TRIS 20 mM; sodium chloride 120 mM; DTT 5 mM; Protein, [U-98% 15N], 500 uM; H2O 90%; D2O 10%

sample_2: TRIS 20 mM; sodium chloride 120 mM; DTT 5 mM; Protein, [U-98% 13C; U-98% 15N], 500 uM; H2O 90%; D2O 10%

sample_3: TRIS 20 mM; sodium chloride 120 mM; DTT 5 mM; Protein, [U-98% 13C; U-98% 15N], 500 uM; D2O 100%

sample_conditions_1: ionic strength: 0.120 M; pH: 7.25; 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_3	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_3	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_3	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_3	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_2	isotropic	sample_conditions_1
3D HNCA	sample_2	isotropic	sample_conditions_1
3D HN(CO)CA	sample_2	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_2	isotropic	sample_conditions_1
3D HNCO	sample_2	isotropic	sample_conditions_1
3D HNHA	sample_2	isotropic	sample_conditions_1
3D C(CO)NH	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_2	isotropic	sample_conditions_1
2D (HB)CB(CGCD)HD	sample_2	isotropic	sample_conditions_1
2D (HB)CB(CGCDCE)HE	sample_2	isotropic	sample_conditions_1

Software:

VNMRJ vVarian VnmrJ 2.2D, Varian - collection

NMRPipe v2011.084.20.33, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRDraw vVer 5.7 Rev 2011.084.20.33, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRView v8.2.33 with Java 1.6.0_31, Johnson, One Moon Scientific - chemical shift assignment, data analysis, peak picking

CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution

X-PLOR NIH v2.31, Schwieters, Kuszewski, Tjandra and Clore - refinement

TALOS vTALOSPlus, Cornilescu, Delaglio and Bax - geometry optimization

Procheck v3.5.4, Laskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Tho - data analysis

NMR spectrometers:

Varian INOVA 600 MHz

BMRB	18990
PDB	2LWR 2M48
GB	AAL13983 AAM18800 AAM43930 AAN12154 AAN12155
REF	NP_730600 NP_730601 XP_001956965 XP_001973584 XP_001984548