BMRB Entry 30456

Name: Solution structure of Trigger Factor dimer
Published: 2018-06-07

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PDB ID: 6d6s
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30456
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:

Solution structure of Trigger Factor dimer

Deposition date:

2018-04-22

Original release date:

2018-06-07

Authors:

Saio, T.; Kawagoe, S.; Ishimori, K.; Kalodimos, C.

Citation:

Citation: Saio, T.; Kawagoe, S.; Ishimori, K.; Kalodimos, C.. "Oligomerization of a molecular chaperone modulates its activity." Elife 7, e35731-e35731 (2018).
PubMed: 29714686

Assembly members:

Assembly members:
entity_1, polymer, 443 residues, 49696.199 Da.

Natural source:

Natural source: Common Name: E. coli Taxonomy ID: 83334 Superkingdom: Bacteria Kingdom: not available Genus/species: Escherichia coli

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MNHKVHHHHHHMQVSVETTQ GLGRRVTITIAADSIETAVK SELVNVAKKVRIDGFRKGKV PMNIVAQRYGASVRQDVLGD LMSRNFIDAIIKEKINPAGA PTYVPGEYKLGEDFTYSVEF EVYPEVELQGLEAIEVEKPI VEVTDADVDGMLDTLRKQQA TWKEKDGAVEAEDRVTIDFT GSVDGEEFEGGKASDFVLAM GQGRMIPGFEDGIKGHKAGE EFTIDVTFPEEYHAENLKGK AAKFAINLKKVEERELPELT AEFIKRFGVEDGSVEGLRAE VRKNMERELKSAIRNRVKSQ AIEGLVKANDIDVPAALIDS EIDVLRRQAAQRFGGNEKQA LELPRELFEEQAKRRVVVGL LLGEVIRTNELKADEERVKG LIEEMASAYEDPKEVIEFYS KNKELMDNMRNVALEEQAVE AVLAKAKVTEKETTFNELMN QQA

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	280
15N chemical shifts	331
1H chemical shifts	1059

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1, 1	1
2	entity_1, 2	1

Entities:

Entity 1, entity_1, 1 443 residues - 49696.199 Da.

1

MET

ASN

HIS

LYS

VAL

HIS

2

HIS

MET

GLN

VAL

SER

VAL

GLU

THR

GLN

3

GLY

LEU

GLY

ARG

VAL

THR

ILE

THR

ILE

4

ALA

ASP

SER

ILE

GLU

THR

ALA

VAL

LYS

5

SER

GLU

LEU

VAL

ASN

VAL

ALA

LYS

VAL

6

ARG

ILE

ASP

GLY

PHE

ARG

LYS

GLY

LYS

VAL

7

PRO

MET

ASN

ILE

VAL

ALA

GLN

ARG

TYR

GLY

8

ALA

SER

VAL

ARG

GLN

ASP

VAL

LEU

GLY

ASP

9

LEU

MET

SER

ARG

ASN

PHE

ILE

ASP

ALA

ILE

10

ILE

LYS

GLU

LYS

ILE

ASN

PRO

ALA

GLY

ALA

11

PRO

THR

TYR

VAL

PRO

GLY

GLU

TYR

LYS

LEU

12

GLY

GLU

ASP

PHE

THR

TYR

SER

VAL

GLU

PHE

13

GLU

VAL

TYR

PRO

GLU

VAL

GLU

LEU

GLN

GLY

14

LEU

GLU

ALA

ILE

GLU

VAL

GLU

LYS

PRO

ILE

15

VAL

GLU

VAL

THR

ASP

ALA

ASP

VAL

ASP

GLY

16

MET

LEU

ASP

THR

LEU

ARG

LYS

GLN

ALA

17

THR

TRP

LYS

GLU

LYS

ASP

GLY

ALA

VAL

GLU

18

ALA

GLU

ASP

ARG

VAL

THR

ILE

ASP

PHE

THR

19

GLY

SER

VAL

ASP

GLY

GLU

PHE

GLU

GLY

20

GLY

LYS

ALA

SER

ASP

PHE

VAL

LEU

ALA

MET

21

GLY

GLN

GLY

ARG

MET

ILE

PRO

GLY

PHE

GLU

22

ASP

GLY

ILE

LYS

GLY

HIS

LYS

ALA

GLY

GLU

23

GLU

PHE

THR

ILE

ASP

VAL

THR

PHE

PRO

GLU

24

GLU

TYR

HIS

ALA

GLU

ASN

LEU

LYS

GLY

LYS

25

ALA

LYS

PHE

ALA

ILE

ASN

LEU

LYS

26

VAL

GLU

ARG

GLU

LEU

PRO

GLU

LEU

THR

27

ALA

GLU

PHE

ILE

LYS

ARG

PHE

GLY

VAL

GLU

28

ASP

GLY

SER

VAL

GLU

GLY

LEU

ARG

ALA

GLU

29

VAL

ARG

LYS

ASN

MET

GLU

ARG

GLU

LEU

LYS

30

SER

ALA

ILE

ARG

ASN

ARG

VAL

LYS

SER

GLN

31

ALA

ILE

GLU

GLY

LEU

VAL

LYS

ALA

ASN

ASP

32

ILE

ASP

VAL

PRO

ALA

LEU

ILE

ASP

SER

33

GLU

ILE

ASP

VAL

LEU

ARG

GLN

ALA

34

GLN

ARG

PHE

GLY

ASN

GLU

LYS

GLN

ALA

35

LEU

GLU

LEU

PRO

ARG

GLU

LEU

PHE

GLU

36

GLN

ALA

LYS

ARG

VAL

GLY

LEU

37

LEU

GLY

GLU

VAL

ILE

ARG

THR

ASN

GLU

38

LEU

LYS

ALA

ASP

GLU

ARG

VAL

LYS

GLY

39

LEU

ILE

GLU

MET

ALA

SER

ALA

TYR

GLU

40

ASP

PRO

LYS

GLU

VAL

ILE

GLU

PHE

TYR

SER

41

LYS

ASN

LYS

GLU

LEU

MET

ASP

ASN

MET

ARG

42

ASN

VAL

ALA

LEU

GLU

GLN

ALA

VAL

GLU

43

ALA

VAL

LEU

ALA

LYS

ALA

LYS

VAL

THR

GLU

44

LYS

GLU

THR

PHE

ASN

GLU

LEU

MET

ASN

45

GLN

ALA

Samples:

sample_1: TF, [U-2H; Ala-13CH3; Met-13CH3; Ile-d1-13CH3; Leu/Val-13CH3/13CH3; Phe-13C15N; Tyr-13C15N], 2.2 mM

sample_2: TF, [Leu/Val-13CH3/13CH3; Phe-13C15N; Tyr-13C15N], 0.6 mM; Trigger Factor, [U-2H; Ala-13CH3; Met-13CH3; Ile-d1-13CH3], 0.6 mM

sample_3: RBD, [U-2H; Ala-13CH3; Met-13CH3; Ile-d1-13CH3; Leu/Val-13CH3/13CH3; Phe-13C15N; Tyr-13C15N], 0.3 mM; PPD-SBD, [U-2H; Ala-13CH3; Met-13CH3; Ile-d1-13CH3; Leu/Val-13CH3/13CH3], 0.3 mM

sample_4: RBD, [U-2H; Ala-13CH3; Met-13CH3; Ile-d1-13CH3; Leu/Val-13CH3/13CH3; Phe-13C15N; Tyr-13C15N], 0.3 mM

sample_5: PPD, [U-99% 13C; U-99% 15N], 0.8 mM

sample_6: SBD, [U-2H; Ala-13CH3; Met-13CH3; Ile-d1-13CH3; Leu/Val-13CH3/13CH3; Phe-13C15N; Tyr-13C15N], 0.5 mM

sample_conditions_1: ionic strength: 100 mM; pH: 7.0; pressure: 1 atm; temperature: 295 K

sample_conditions_2: ionic strength: 100 mM; pH: 7.0; pressure: 1 atm; temperature: 283 K

sample_conditions_3: ionic strength: 100 mM; pH: 7.0; pressure: 1 atm; temperature: 308 K

sample_conditions_4: ionic strength: 100 mM; pH: 7.0 pD; pressure: 1 atm; temperature: 295 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D (1H)-13C HMQC-NOESY-1H-13C HMQC	sample_1	isotropic	sample_conditions_1
3D (1H)-13C HMQC-NOESY-1H-13C HMQC	sample_1	isotropic	sample_conditions_2
3D (1H)-13C HMQC-NOESY-1H-13C HMQC	sample_1	isotropic	sample_conditions_3
3D-SOFAST-(1H)-13C HMQC-NOESY-1H-13C HMQC	sample_2	isotropic	sample_conditions_4
13C-edited SOFAST-NOESY-HMQC	sample_2	isotropic	sample_conditions_4
3D (1H)-13C HMQC-NOESY-1H-13C HMQC	sample_3	isotropic	sample_conditions_4
3D-SOFAST-(1H)-13C HMQC-NOESY-1H-13C HMQC	sample_3	isotropic	sample_conditions_4
13C-edited SOFAST-NOESY-HMQC	sample_3	isotropic	sample_conditions_4
3D (1H)-13C HMQC-NOESY-1H-13C HMQC	sample_6	isotropic	sample_conditions_1
3D (1H)-15N HMQC-NOESY-1H-13C HMQC	sample_6	isotropic	sample_conditions_1
3D (1H)-13C HMQC-NOESY-1H-15N HMQC	sample_6	isotropic	sample_conditions_1
13C-edited NOESY-HMQC	sample_6	isotropic	sample_conditions_4
15N-edited NOESY-HSQC	sample_6	isotropic	sample_conditions_1
13C-edited NOESY-HSQC	sample_5	isotropic	sample_conditions_1
15N-edited NOESY-HSQC	sample_5	isotropic	sample_conditions_1
3D (1H)-13C HMQC-NOESY-1H-13C HMQC	sample_4	isotropic	sample_conditions_1
13C-edited NOESY-HSQC	sample_4	isotropic	sample_conditions_1
2D 1H-13C HMQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HMQC	sample_1	isotropic	sample_conditions_2
2D 1H-13C HMQC	sample_1	isotropic	sample_conditions_3
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_4

Software:

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

OLIVIA, Masashi Yokochi - chemical shift assignment

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

NMR spectrometers:

Bruker AvanceIII 800 MHz
Bruker AvanceIII 700 MHz
Bruker AvanceIII 600 MHz
Varian UNITY 800 MHz
Varian UNITY 600 MHz

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