BMRBj - BMREntryMaster

Found 1 Document (1.572 seconds)

BMRB: 6838

1G68

1H, 13C and 15N backbone resonance assignment for PSE-4, a 29.5 kDa class A beta-lactamase from Pseudomonas aeruginosa

Authors

Morin, S., Levesque, R.C., Gagne, S.M.

Assembly

PSE-4

Entity

1. PSE-4 (polymer, Thiol state: all disulfide bound), 271 monomers, 29526.89 Da Detail

SSSKFQQVEQ DVKAIEVSLS ARIGVSVLDT QNGEYWDYNG NQRFPLTSTF KTIACAKLLY DAEQGKVNPN STVEIKKADL VTYSPVIEKQ VGQAITLDDA CFATMTTSDN TAANIILSAV GGPKGVTDFL RQIGDKETRL DRIEPDLNEG KLGDLRDTTT PKAIASTLNK FLFGSALSEM NQKKLESWMV NNQVTGNLLR SVLPAGWNIA DRSGAGGFGA RSITAVVWSE HQAPIIVSIY LAQTQASMEE RNDAIVKIGH SIFDVYTSQS R

Formula weight

29526.89 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS55:SG	1:CYS101:SG

Source organism

Pseudomonas aeruginosa

Exptl. method

solution NMR

Data set

assigned_chemical_shifts, heteronucl_NOEs, heteronucl_T1_relaxation, heteronucl_T2_relaxation, H_exch_protection_factors, H_exch_rates, order_parameters

Chem. Shift Complete

Sequence coverage: 99.6 %, Completeness: 48.9 %, Completeness (bb): 83.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	48.9 % (1501 of 3071)	26.5 % (419 of 1583)	68.8 % (820 of 1191)	88.2 % (262 of 297)
Backbone	83.1 % (1338 of 1610)	54.1 % (299 of 553)	98.1 % (779 of 794)	98.9 % (260 of 263)
Sidechain	23.9 % (409 of 1713)	11.7 % (120 of 1030)	44.2 % (287 of 649)	5.9 % (2 of 34)
Aromatic	4.1 % (8 of 194)	4.1 % (4 of 97)	4.3 % (4 of 93)	0.0 % (0 of 4)
Methyl	20.3 % (67 of 330)	15.8 % (26 of 165)	24.8 % (41 of 165)

1. PSE-4 mature enzyme

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Temperature 303.15 (±0.1) K, pH 6.65 (±0.05), Details PSE-4 0.6 mM (U-98% 13C, U-96% 15N) DSS 0.1 mM Imidazole 3 mM Sodium azide 0.1% D2O 10% H2O 90% Protease inhibitors cocktail pH 6.65

#	Name	Isotope labeling	Type	Concentration
1	PSE-4	[U-98% 13C; U-96% 15N]	protein	0.6 mM
2	DSS	natural abundance		0.1 mM
3	Imidazole	natural abundance		3 mM
4	Sodium azide	natural abundance		0.1 %
5	D2O	natural abundance		10 %
6	H2O	natural abundance		90 %
7	Protease inhibitors cocktail	natural abundance		0.1 mM

Sample #2

Solvent system 90% H2O/10% D2O, Temperature 303.15 (±0.1) K, pH 6.65 (±0.05), Details PSE-4 0.6 mM (U-91% 2H, U-98% 13C, U-96% 15N) DSS 0.1 mM Imidazole 3 mM Sodium azide 0.1% D2O 10% H2O 90% Protease inhibitors cocktail pH 6.65

#	Name	Isotope labeling	Type	Concentration
8	PSE-4	[U-91% 2H; U-98% 13C; U-96% 15N]	protein	0.6 mM
9	DSS	natural abundance		0.1 mM
10	Imidazole	natural abundance		3 mM
11	Sodium azide	natural abundance		0.1 %
12	D2O	natural abundance		10 %
13	H2O	natural abundance		90 %
14	Protease inhibitors cocktail	natural abundance		0.1 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.15 ppm, Outliers: 5 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.15 ppm, Outliers: 5 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.02 ppm, Outliers: 2 Detail

Heteronucl. T₁

703 T₁ values in 3 lists
Coherence Sz, Field strength (¹H) 500 MHz, 600 MHz, 800 MHz, Temperature 304.65 (±0.1) K, pH 6.65 (±0.05) Detail

Heteronucl. T₂

701 T₂ values in 3 lists
Coherence S(+,-), Field strength (¹H) 500 MHz, 600 MHz, 800 MHz, Temperature 304.65 (±0.1) K, pH 6.65 (±0.05) Detail

Heteronucl. NOE

703 NOE values in 3 lists
Value type relative intensities, Field strength (¹H) 500 MHz, 600 MHz, 800 MHz, Temperature 304.65 (±0.1) K, pH 6.65 (±0.05) Detail

Heteronucl. T₁/T₂

701 T₁/T₂ values in 3 lists
Field strength (¹H) 500 MHz, 600 MHz, 800 MHz, Temperature 304.65 (±0.1) K, pH 6.65 (±0.05) Detail

Order parameters

230 S² values in 1 lists
Temperature 304.65 (±0.1) K, pH 6.65 (±0.05) Detail

¹H exch. protect.

262 values in 1 lists
Temperature 304.65 (±0.1) K, pH 6.65 (±0.05) Detail

¹H exchange rate

420 k_ex values in 2 lists
Temperature 304.65 (±0.1) K, pH 6.65 (±0.05), 7.85 (±0.05) Detail

Release date

2006-05-01

Citation 1

NMR dynamics of PSE-4 beta-lactamase: an interplay of ps-ns order and mus-ms motions in the active site
Morin, S., Gagne, S.M.
Biophys. J. (2009), 96, 4681-4691, PubMed 19486690 , DOI 10.1016/j.bpj.2009.02.068 , Abstract

Show more 6 citaions

Citation 2

Smartnotebook: a semi-automated approach to protein sequential NMR resonance assignments
Slupsky, C.M., Boyko, R.F., Booth, V.K., Sykes, B.D.
J. Biomol. NMR (2003), 27, 313-321, PubMed 14512729 , Abstract

Citation 3

NMRView: A computer program for the visualization and analysis of NMR data
Johnson, B.A., Blevins, R.A.
J. Biomol. NMR (1994), 4, 603-614

Citation 4

NMRPipe: a multidimensional spectral processing system based on UNIX pipes
Delaglio, F., Grzesiek, S., Vuister, G.W., Zhu, G., Pfeifer, J., Bax, A.
J. Biomol. NMR (1995), 6, 277-293, PubMed 8520220 , Abstract

Citation 5

Carbenicillin-resistant pseudomonas
Newsom, S.W.B.
Lancet (1969), 2, 1141-1141, PubMed 4188085 , Abstract

Citation 6

Insights into the molecular basis for the carbenicillinase activity of PSE-4 beta-lactamase from crystallographic and kinetic studies
Lim, D., Sanschagrin, F., Passmore, L., De Castro, L., Levesque, R.C., Strynadka, N.C.
Biochemistry (2001), 40, 395-402, PubMed 11148033 , DOI: , Abstract

Citation 7

1H, 13C, and 15N backbone resonance assignments for PSE-4, a 29.5 kDa class A beta-lactamase from Pseudomonas aeruginosa
Morin, S., Levesque, R.C., Gagne, S.M.
J. Biomol. NMR (2006), 36 Suppl 1, 11-11, PubMed 16642403 , DOI 10.1007/s10858-005-5343-7 , Abstract

Hide non-primary 6 citaions

Related entities 1. PSE-4, : 1 : 1 : 1 : 2 : 165 entities Detail

Experiments performed 12 experiments Detail

1 15N-TROSY-HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 303.15 (±0.1) K, pH 6.65 (±0.05), Details PSE-4 0.6 mM (U-98% 13C, U-96% 15N) DSS 0.1 mM Imidazole 3 mM Sodium azide 0.1% D2O 10% H2O 90% Protease inhibitors cocktail pH 6.65

#	Name	Isotope labeling	Type	Concentration
1	PSE-4	[U-98% 13C; U-96% 15N]	protein	0.6 mM
2	DSS	natural abundance		0.1 mM
3	Imidazole	natural abundance		3 mM
4	Sodium azide	natural abundance		0.1 %
5	D2O	natural abundance		10 %
6	H2O	natural abundance		90 %
7	Protease inhibitors cocktail	natural abundance		0.1 mM

2 TROSY-HNCO

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	PSE-4	[U-98% 13C; U-96% 15N]	protein	0.6 mM
2	DSS	natural abundance		0.1 mM
3	Imidazole	natural abundance		3 mM
4	Sodium azide	natural abundance		0.1 %
5	D2O	natural abundance		10 %
6	H2O	natural abundance		90 %
7	Protease inhibitors cocktail	natural abundance		0.1 mM

3 TROSY-HN(CA)CO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 303.15 (±0.1) K, pH 6.65 (±0.05), Details PSE-4 0.6 mM (U-91% 2H, U-98% 13C, U-96% 15N) DSS 0.1 mM Imidazole 3 mM Sodium azide 0.1% D2O 10% H2O 90% Protease inhibitors cocktail pH 6.65

#	Name	Isotope labeling	Type	Concentration
8	PSE-4	[U-91% 2H; U-98% 13C; U-96% 15N]	protein	0.6 mM
9	DSS	natural abundance		0.1 mM
10	Imidazole	natural abundance		3 mM
11	Sodium azide	natural abundance		0.1 %
12	D2O	natural abundance		10 %
13	H2O	natural abundance		90 %
14	Protease inhibitors cocktail	natural abundance		0.1 mM

4 TROSY-HNCA

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	PSE-4	[U-98% 13C; U-96% 15N]	protein	0.6 mM
2	DSS	natural abundance		0.1 mM
3	Imidazole	natural abundance		3 mM
4	Sodium azide	natural abundance		0.1 %
5	D2O	natural abundance		10 %
6	H2O	natural abundance		90 %
7	Protease inhibitors cocktail	natural abundance		0.1 mM

5 TROSY-HN(CO)CA

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	PSE-4	[U-98% 13C; U-96% 15N]	protein	0.6 mM
2	DSS	natural abundance		0.1 mM
3	Imidazole	natural abundance		3 mM
4	Sodium azide	natural abundance		0.1 %
5	D2O	natural abundance		10 %
6	H2O	natural abundance		90 %
7	Protease inhibitors cocktail	natural abundance		0.1 mM

6 TROSY-HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
8	PSE-4	[U-91% 2H; U-98% 13C; U-96% 15N]	protein	0.6 mM
9	DSS	natural abundance		0.1 mM
10	Imidazole	natural abundance		3 mM
11	Sodium azide	natural abundance		0.1 %
12	D2O	natural abundance		10 %
13	H2O	natural abundance		90 %
14	Protease inhibitors cocktail	natural abundance		0.1 mM

7 TROSY-CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	PSE-4	[U-98% 13C; U-96% 15N]	protein	0.6 mM
2	DSS	natural abundance		0.1 mM
3	Imidazole	natural abundance		3 mM
4	Sodium azide	natural abundance		0.1 %
5	D2O	natural abundance		10 %
6	H2O	natural abundance		90 %
7	Protease inhibitors cocktail	natural abundance		0.1 mM

8 15N-T1

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Temperature 304.65 (±0.1) K, pH 6.65 (±0.05), Details PSE-4 0.5 mM (U-96% 15N) Imidazole 3 mM Sodium azide 0.1% D2O 10% H2O 90% pH 6.65

#	Name	Isotope labeling	Type	Concentration
22	PSE-4	[U-96% 15N]	protein	0.6 mM
23	Imidazole	natural abundance		3 mM
24	Sodium azide	natural abundance		0.1 %
25	D2O	natural abundance		10 %
26	H2O	natural abundance		90 %

9 15N-T2

Instrument

Varian INOVA - 500 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
22	PSE-4	[U-96% 15N]	protein	0.6 mM
23	Imidazole	natural abundance		3 mM
24	Sodium azide	natural abundance		0.1 %
25	D2O	natural abundance		10 %
26	H2O	natural abundance		90 %

10 1H-15N-NOE

Instrument

Varian INOVA - 500 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
22	PSE-4	[U-96% 15N]	protein	0.6 mM
23	Imidazole	natural abundance		3 mM
24	Sodium azide	natural abundance		0.1 %
25	D2O	natural abundance		10 %
26	H2O	natural abundance		90 %

11 15N-TROSY-HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 0% H2O/100% D2O, Temperature 304.65 (±0.1) K, pH 6.65 (±0.05), Details PSE-4 0.5 mM (U-96% 15N) Imidazole 3 mM Sodium azide 0.1% D2O 100% H2O 0% pH 6.65

#	Name	Isotope labeling	Type	Concentration
27	PSE-4	[U-96% 15N]	protein	0.5 mM
28	Imidazole	natural abundance		3 mM
29	Sodium azide	natural abundance		0.1 %
30	D2O	natural abundance		100 %

12 15N-TROSY-HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 0% H2O/100% D2O, Temperature 304.65 (±0.1) K, pH 7.85 (±0.05), Details PSE-4 0.5 mM (U-96% 15N) Imidazole 3 mM Sodium azide 0.1% D2O 100% H2O 0% pH 7.85

#	Name	Isotope labeling	Type	Concentration
31	PSE-4	[U-96% 15N]	protein	0.5 mM
32	Imidazole	natural abundance		3 mM
33	Sodium azide	natural abundance		0.1 %
34	D2O	natural abundance		100 %

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts, Heteronucl NOE exptl data, Heteronucl T1 relaxation data, Heteronucl T2 relaxation data, Order parameter relaxation analysis	bmr6838_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:55:CYS:SG	1:101:CYS:SG	oxidized, CA 61.652, CB 41.607 ppm	oxidized, CA 63.781, CB 42.009 ppm	n/a

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Content subtype: bmr6838_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	chem_shift_list_1	Warning	1298		99.3 (chain: 1, length: 271)
1	Chemical shift references	chemical_shift_referencing	OK	3		No information

Assigned chemical shifts

Saveframe: chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 271, Sequence coverage: 99.3%
- Total number of assignments
  - ¹³C chemical shifts: 782
  - ¹H chemical shifts: 258
  - ¹⁵N chemical shifts: 258
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- Peptide bond of PRO
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	1191	782	65.7
¹H chemical shifts	1583	258	16.3
¹⁵N chemical shifts	308	258	83.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	542	535	98.7
¹H chemical shifts	553	258	46.7
¹⁵N chemical shifts	263	258	98.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	649	247	38.1
¹H chemical shifts	1030	0	0.0
¹⁵N chemical shifts	45	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	169	24	14.2
¹H chemical shifts	169	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	93	0	0.0
¹H chemical shifts	97	0	0.0
¹⁵N chemical shifts	4	0	0.0

Keywords antibiotic resistance, backbone dynamics, class A beta-lactamase, liquid-state NMR, PSE-4, Pseudomonas aeruginosa, nmr chemical shift assignment, visualization and analysis of nmr data, processing nmr data, Carbenicillin-resistant pseudomonas, PSE-4 crystal structure, chemical shift assignment

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (1.572 seconds)

BMRB: 6838

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. PSE-4, : 1 : 1 : 1 : 2 : 165 entities Detail

Experiments performed 12 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Chemical shift validation 3 contents Detail