BMRB Entry 19315

Name: Solution Structure of the Catalytic Domain of HHARI
Published: 2013-11-11

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PDB ID: 2m9y
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19315
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution Structure of the Catalytic Domain of HHARI

Deposition date:

2013-07-09

Original release date:

2013-11-11

Authors:

Mercier, Pascal; Spratt, Donald; Shaw, Gary

Citation:

Citation: Spratt, Donald; Mercier, Pascal; Gary, Shaw. "Structure of the HHARI catalytic domain shows glimpses of a HECT E3 ligase" PLoS ONE 8, e74047-e74047 (2013).
PubMed: 24058416

Assembly members:

Assembly members:
entity_1, polymer, 74 residues, 8439.303 Da.
entity_ZN, non-polymer, 65.409 Da.

Natural source:

Natural source: Common Name: E. coli Taxonomy ID: 562 Superkingdom: Bacteria Kingdom: not available Genus/species: Escherichia coli

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GSKKCDDDSETSNWIAANTK ECPKCHVTIEKDGGSNHMVC RNQNCKAEFCWVCLGPWEPH GSAWYNCNRYNEDD

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	222
15N chemical shifts	87
1H chemical shifts	420

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	HHARI Catalytic Domain	1
2	ZINC ION_1	2
3	ZINC ION_2	2

Entities:

Entity 1, HHARI Catalytic Domain 74 residues - 8439.303 Da.

Residues 323-324 (N-terminal "GS") results from cloning and remains in the intact protein after TEV cleavage.

1

GLY

SER

LYS

CYS

ASP

SER

GLU

2

THR

SER

ASN

TRP

ILE

ALA

ASN

THR

LYS

3

GLU

CYS

PRO

LYS

CYS

HIS

VAL

THR

ILE

GLU

4

LYS

ASP

GLY

SER

ASN

HIS

MET

VAL

CYS

5

ARG

ASN

GLN

ASN

CYS

LYS

ALA

GLU

PHE

CYS

6

TRP

VAL

CYS

LEU

GLY

PRO

TRP

GLU

PRO

HIS

7

GLY

SER

ALA

TRP

TYR

ASN

CYS

ASN

ARG

TYR

8

ASN

GLU

ASP

Entity 2, ZINC ION_1 - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: MES 20 mM; sodium chloride 120 mM; DTT 5 mM; entity_1, [U-98% 15N], 2.3 mM

sample_2: MES 20 mM; sodium chloride 120 mM; DTT 5 mM; entity_1, [U-98% 13C; U-98% 15N], 2.3 mM

sample_conditions_1: ionic strength: 0.120 M; 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_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_2	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_2	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	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
2D HCN	sample_2	isotropic	sample_conditions_1

Software:

VNMRJ vVarian VnmrJ 2.2D, Varian - collection

NMRPipe v2013.021.23.09, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRDraw vVer 7.9 Rev 2013.021.23.09, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRView v9.0.0beta76, Johnson, One Moon Scientific - chemical shift assignment, data analysis, peak picking

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

X-PLOR NIH v2.33, Schwieters, Kuszewski, Tjandra and Clore - refinement

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

NMR spectrometers:

Varian INOVA 600 MHz

PDB	1WD2 2M9Y 4KBL 4KC9
DBJ	BAD92669 BAG35590
EMBL	CAA08817 CAA10274 CAB45870 CAF98343 CAH65069
GB	AAD28088 AAH38034 AAH51877 AAH57523 AAH57680
REF	NP_001013126 NP_001025558 NP_001075183 NP_001089823 NP_001116952
SP	A2VEA3 B1H1E4 Q32NS4 Q6NW85 Q6PFJ9
TPG	DAA25726
AlphaFold	A2VEA3 B1H1E4 Q32NS4 Q6NW85 Q6PFJ9