BMRB Entry 17610

Name: Solution structure of GppNHp-bound H-RasT35S mutant protein.
Published: 2012-05-09

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PDB ID: 2n46
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR17610
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution structure of GppNHp-bound H-RasT35S mutant protein.

Deposition date:

2011-04-28

Original release date:

2012-05-09

Authors:

Araki, Mitsugu

Citation:

Citation: Araki, Mitsugu; Shima, Fumi; Yoshikawa, Yoko; Muraoka, Shin; Ijiri, Yuichi; Nagahara, Yuka; Shirono, Tomoya; Kataoka, Tohru; Tamura, Atsuo. "Solution structure of the state 1 conformer of GTP-bound H-Ras protein and distinct dynamic properties between the state 1 and state 2 conformers." J. Biol. Chem. 286, 39644-39653 (2011).
PubMed: 21930707

Assembly members:

Assembly members:
GppNHp-bound H-RasT35S mutant protein, polymer, 172 residues, 18861.303 Da.
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER, non-polymer, 522.196 Da.
MG, non-polymer, 24.305 Da.

Natural source:

Natural source: Common Name: human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
GppNHp-bound H-RasT35S mutant protein: GPLGSDMTEYKLVVVGAGGV GKSALTIQLIQNHFVDEYDP SIEDSYRKQVVIDGETCLLD ILDTAGQEEYSAMRDQYMRT GEGFLCVFAINNTKSFEDIH QYREQIKRVKDSDDVPMVLV GNKCDLAARTVESRQAQDLA RSYGIPYIETSAKTRQGVED AFYTLVREIRQH

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

Data type	Count
13C chemical shifts	719
15N chemical shifts	184
1H chemical shifts	1177
T1 relaxation values	130
T2 relaxation values	130
heteronuclear NOE values	130

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	GppNHp-bound H-RasT35S mutant protein	1
2	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER	2
3	magnesium ions	3

Entities:

Entity 1, GppNHp-bound H-RasT35S mutant protein 172 residues - 18861.303 Da.

1

GLY

PRO

LEU

GLY

SER

ASP

MET

THR

GLU

TYR

2

LYS

LEU

VAL

GLY

ALA

GLY

VAL

3

GLY

LYS

SER

ALA

LEU

THR

ILE

GLN

LEU

ILE

4

GLN

ASN

HIS

PHE

VAL

ASP

GLU

TYR

ASP

PRO

5

SER

ILE

GLU

ASP

SER

TYR

ARG

LYS

GLN

VAL

6

VAL

ILE

ASP

GLY

GLU

THR

CYS

LEU

ASP

7

ILE

LEU

ASP

THR

ALA

GLY

GLN

GLU

TYR

8

SER

ALA

MET

ARG

ASP

GLN

TYR

MET

ARG

THR

9

GLY

GLU

GLY

PHE

LEU

CYS

VAL

PHE

ALA

ILE

10

ASN

THR

LYS

SER

PHE

GLU

ASP

ILE

HIS

11

GLN

TYR

ARG

GLU

GLN

ILE

LYS

ARG

VAL

LYS

12

ASP

SER

ASP

VAL

PRO

MET

VAL

LEU

VAL

13

GLY

ASN

LYS

CYS

ASP

LEU

ALA

ARG

THR

14

VAL

GLU

SER

ARG

GLN

ALA

GLN

ASP

LEU

ALA

15

ARG

SER

TYR

GLY

ILE

PRO

TYR

ILE

GLU

THR

16

SER

ALA

LYS

THR

ARG

GLN

GLY

VAL

GLU

ASP

17

ALA

PHE

TYR

THR

LEU

VAL

ARG

GLU

ILE

ARG

18

GLN

HIS

Entity 2, PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER - C10 H17 N6 O13 P3 - 522.196 Da.

1

GNP

Entity 3, magnesium ions - Mg - 24.305 Da.

1

MG

Samples:

sample_1: GppNHp-bound H-RasT35S mutant protein, [U-98% 13C; U-98% 15N], 1 – 2 mM; PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER1 – 2 mM; magnesium ions 10 mM; sodium chloride 150 mM; sodium phosphate 25 mM; H20 90%; D2O 10%

sample_2: GppNHp-bound H-RasT35S mutant protein, [U-98% 13C; U-98% 15N], 1 – 2 mM; PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER1 – 2 mM; magnesium ions 10 mM; sodium chloride 150 mM; sodium phosphate 25 mM; H20 90%; D2O 10%

sample_conditions_1: ionic strength: 0.24 M; pH: 6.8; pressure: 1 atm; temperature: 298 K

Experiments:

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

Software:

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

CNS v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY, Goddard - peak picking

NMR spectrometers:

Bruker DMX 750 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks