BMRB Entry 17496

Name: Solution Structure of the PilZ Domain Protein PA4608 Complex with Cyclic Di-GMP Identifies Charge Clustering as Molecular Readout
Published: 2011-06-01

Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR17496

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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 the PilZ Domain Protein PA4608 Complex with Cyclic Di-GMP Identifies Charge Clustering as Molecular Readout

Deposition date:

2011-02-28

Original release date:

2011-06-01

Authors:

Habazettl, Judith; Allan, Martin; Jenal, Urs; Grzesiek, Stephan

Citation:

Citation: Habazettl, Judith; Allan, Martin; Jenal, Urs; Grzesiek, Stephan. "Solution Structure of the PilZ Domain Protein PA4608 Complex with Cyclic di-GMP Identifies Charge Clustering as Molecular Readout." J. Biol. Chem. 286, 14304-14314 (2011).
PubMed: 21310957

Assembly members:

Assembly members:
PA4608, polymer, 145 residues, 14593.500 Da.
C2E, non-polymer, 690.411 Da.

Natural source:

Natural source: Common Name: Pseudomonas aeruginosa Taxonomy ID: 287 Superkingdom: Bacteria Kingdom: not available Genus/species: Pseudomonas aeruginosa

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET15

Entity Sequences (FASTA):

Entity Sequences (FASTA):
PA4608: MGSSHHHHHHSSGLVPRGSH MSDQHDERRRFHRIAFDADS EILQGERRWEVLLHDVSLHG ILVGQPQDWNGDPQRPFEAR LYLGLDVLIRMEISLAWARD GLLGFECQHIDLDSISHLRR LVELNLGDEELLERELALLV SAHDD

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	573
15N chemical shifts	153
1H chemical shifts	918

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	PA4608	1
2	C2E_1	2
3	C2E_2	2

Entities:

Entity 1, PA4608 145 residues - 14593.500 Da.

1

MET

GLY

SER

HIS

2

SER

GLY

LEU

VAL

PRO

ARG

GLY

SER

HIS

3

MET

SER

ASP

GLN

HIS

ASP

GLU

ARG

4

PHE

HIS

ARG

ILE

ALA

PHE

ASP

ALA

ASP

SER

5

GLU

ILE

LEU

GLN

GLY

GLU

ARG

TRP

GLU

6

VAL

LEU

HIS

ASP

VAL

SER

LEU

HIS

GLY

7

ILE

LEU

VAL

GLY

GLN

PRO

GLN

ASP

TRP

ASN

8

GLY

ASP

PRO

GLN

ARG

PRO

PHE

GLU

ALA

ARG

9

LEU

TYR

LEU

GLY

LEU

ASP

VAL

LEU

ILE

ARG

10

MET

GLU

ILE

SER

LEU

ALA

TRP

ALA

ARG

ASP

11

GLY

LEU

GLY

PHE

GLU

CYS

GLN

HIS

ILE

12

ASP

LEU

ASP

SER

ILE

SER

HIS

LEU

ARG

13

LEU

VAL

GLU

LEU

ASN

LEU

GLY

ASP

GLU

14

LEU

GLU

ARG

GLU

LEU

ALA

LEU

VAL

15

SER

ALA

HIS

ASP

Entity 2, C2E_1 - C20 H24 N10 O14 P2 - 690.411 Da.

1

C2E

Samples:

sample_1: sodium chloride 250 mM; TRIS 10 mM; sodium azide 0.01%; PA4608, [U-99% 13C; U-99% 15N], 0.8 mM; C2E 1.6 mM; H2O 95%; D2O 5%

sample_7: sodium chloride 250 mM; TRIS 10 mM; sodium azide 0.01%; PA4608, [U-99% 13C; U-99% 15N], 1.1 mM; H2O 95%; D2O 5%

sample_2: sodium chloride 250 mM; TRIS 10 mM; sodium azide 0.01%; PA4608, [U-99% 13C; U-99% 15N], 0.8 mM; C2E 1.6 mM; D2O 100%

sample_3: sodium chloride 250 mM; TRIS 10 mM; sodium azide 0.01%; PA4608, [U-99% 13C; U-99% 15N], 1.0 mM; C2E, [U-99% 13C; U-99% 15N], 2.0 mM; D2O 100%

sample_4: sodium chloride 250 mM; TRIS 10 mM; sodium azide 0.01%; PA4608, [U-99% 13C; U-99% 15N], 0.6 mM; C2E, [U-99% 13C; U-99% 15N], 1.2 mM; H2O 93%; D2O 7%

sample_5: sodium chloride 250 mM; TRIS 10 mM; sodium azide 0.01%; PA4608, [U-99% 13C; U-99% 15N], 1.0 mM; C2E, [U-99% 13C; U-99% 15N], 2.0 mM; H2O 95%; D2O 5%

sample_6: sodium chloride 250 mM; TRIS 10 mM; sodium azide 0.01%; PA4608, [U-99% 13C; U-99% 15N], 1.2 mM; C2E, [U-99% 13C; U-99% 15N], 0.6 mM; C2E 0.6 mM; H2O 95%; D2O 5%

sample_8: sodium chloride 250 mM; TRIS 10 mM; sodium azide 0.01%; PA4608, [U-99% 15N], 0.5 mM; H2O 95%; D2O 5%

sample_conditions_1: pH: 6.7; pressure: 1 atm; temperature: 293 K

sample_conditions_2: pH: 6.7; pressure: 1 atm; temperature: 313 K

sample_conditions_3: pH: 6.7; pressure: 1 atm; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	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 HCCH-TOCSY (Ribose)	sample_3	isotropic	sample_conditions_1
3D HCCH-COSY (Ribose)	sample_3	isotropic	sample_conditions_3
HAHB	sample_2	isotropic	sample_conditions_1
HAHB (Ribose)	sample_3	isotropic	sample_conditions_1
HAHB (Ribose)	sample_4	anisotropic	sample_conditions_1
13C-{13Cg}spin-echo difference H-15N HSQC	sample_5	isotropic	sample_conditions_1
15N-{13Cg} spin-echo diference H-15N HAQC	sample_5	isotropic	sample_conditions_1
Methyl C	sample_2	isotropic	sample_conditions_1
Methyl N	sample_2	isotropic	sample_conditions_1
3D 1H-15N ROESY	sample_5	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_1	isotropic	sample_conditions_1
3D 1H-13C NOESY(Ribose)	sample_5	isotropic	sample_conditions_1
4D 13C-13C NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY (filtered against H bound to 13C, 15N)	sample_1	isotropic	sample_conditions_1
IPAP 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
IPAP 1H-15N HSQC	sample_4	anisotropic	sample_conditions_1
J-resolved ct 13C-HSQC	sample_5	isotropic	sample_conditions_1
J-resolved ct 13C-HSQC	sample_4	anisotropic	sample_conditions_1
2D H-resolved 15N EXSY	sample_6	isotropic	sample_conditions_1
3D H-15N-15N EXSY	sample_6	isotropic	sample_conditions_2
IPAP 1H-15N HSQC	sample_7	isotropic	sample_conditions_1
IPAP 1H-15N HSQC	sample_8	anisotropic	sample_conditions_1
2D 1H resolved 15N EXSY	sample_6	isotropic	sample_conditions_3
2D 1H-resolved 15N EXSY	sample_6	isotropic	sample_conditions_2
2D 1H-15N HSQC	sample_7	isotropic	sample_conditions_1
15N Relaxation	sample_7	isotropic	sample_conditions_1
15N Relaxation	sample_1	isotropic	sample_conditions_1

Software:

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

PIPP, Garrett - peak picking

SPARKY, Goddard - chemical shift assignment, structure solution

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure solution

NMR spectrometers:

Bruker DRX 600 MHz
Bruker DPX 800 MHz

PDB	1YWU 2L74
DBJ	BAK87859 BAP21553 BAP53111 BAQ42358 BAR70033
EMBL	CAW29747 CCQ83984 CDH73305 CDH79614 CDI93152
GB	AAG07996 ABJ13986 ABR81943 AEO77182 AFM67158
REF	NP_253298 WP_003094864 WP_003123411 WP_003153057 WP_024914602
SP	Q9HVI1
AlphaFold	Q9HVI1