BMRB Entry 6594

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PDB ID: 1z2q
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR6594
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:

Elucidation of the high-resolution solution structure of a trypanosomatid FYVE domain

Deposition date:

2005-04-14

Original release date:

2007-11-14

Authors:

Mertens, H.; Callaghan, J.; McConville, M.; Gooley, P.

Citation:

Citation: Mertens, H.; Callaghan, J.; Swarbrick, J.; McConville, M.; Gooley, P.. "A high-resolution solution structure of a trypanosomatid FYVE domain" Protein Sci. 16, 2552-2559 (2007).

Assembly members:

Assembly members:
Leishmania major FYVE domain containing protein 1, polymer, 84 residues, Formula weight is not available
ZN, non-polymer, 65.409 Da.

Natural source:

Natural source: Common Name: Leishmania major Taxonomy ID: 5664 Superkingdom: Eukaryota Kingdom: not available Genus/species: Leishmania major

Experimental source:

Experimental source: Production method: recombinant technology

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Leishmania major FYVE domain containing protein 1: GPLGSMGEKQSKGYWQEDED APACNGCGCVFTTTVRRHHC RNCGYVLCGDCSRHRAAIPM RGITEPERVCDACYLALRSS NMAG

Data sets:

assigned_chemical_shifts
- chemical_shift_set_1

Data type	Count
13C chemical shifts	323
15N chemical shifts	87
1H chemical shifts	492

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	LM5-1	1
2	ZINC (II) ION, 1	2
3	ZINC (II) ION, 2	2

Entities:

Entity 1, LM5-1 84 residues - Formula weight is not available

1

GLY

PRO

LEU

GLY

SER

MET

GLY

GLU

LYS

GLN

2

SER

LYS

GLY

TYR

TRP

GLN

GLU

ASP

GLU

ASP

3

ALA

PRO

ALA

CYS

ASN

GLY

CYS

GLY

CYS

VAL

4

PHE

THR

VAL

ARG

HIS

CYS

5

ARG

ASN

CYS

GLY

TYR

VAL

LEU

CYS

GLY

ASP

6

CYS

SER

ARG

HIS

ARG

ALA

ILE

PRO

MET

7

ARG

GLY

ILE

THR

GLU

PRO

GLU

ARG

VAL

CYS

8

ASP

ALA

CYS

TYR

LEU

ALA

LEU

ARG

SER

9

ASN

MET

ALA

GLY

Entity 2, ZINC (II) ION, 1 - Zn - 65.409 Da.

1

ZN

Samples:

sample_1: Leishmania major FYVE domain containing protein 1, [U-15N; U-13C], 0.8 mM; sodium phosphate buffer 50 mM; KCl 50 mM; DTT 1 mM; AEBSF 1 mM; sodium azide 0.05%; H2O 90%; D2O 10%

sample_2: Leishmania major FYVE domain containing protein 1, [U-15N; U-13C], 0.8 mM; sodium phosphate buffer 50 mM; KCl 50 mM; DTT 1 mM; AEBSF 1 mM; sodium azide 0.05%; D2O 99.99%

sample_3: Leishmania major FYVE domain containing protein 1, [U-10% 13C], 0.8 mM; sodium phosphate buffer 50 mM; KCl 50 mM; DTT 1 mM; AEBSF 1 mM; sodium azide 0.05%; H2O 90%; D2O 10%

sample_cond_1: pH: 7.4; pressure: 1 atm; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 13C-separated NOESY	not available	not available	sample_cond_1
3D 15N-separated NOESY	not available	not available	sample_cond_1
HNHA	not available	not available	sample_cond_1
2D 13C-ct-HSQC	not available	not available	sample_cond_1

Software:

VNMR v6.1c - collection

NMRPipe v2.2 - processing

XEASY v1.3 - data analysis

CYANA v1.0.7 - structure solution

X-PLOR NIH v2.9.1 - refinement

NMR spectrometers:

Varian INOVA 600 MHz