BMRBj - BMREntryMaster

Found 1 Document (1.305 seconds)

BMRB: 4336

1HPC

Backbone and Sequence-Specific Assignment of Three Forms of the Lipoate Containing H-protein of the Glycine Decarboxylase Complex.

Authors

Guilhaudis, L., Simorre, J., Bouchayer, E., Neuburger, M., Bourguignon, J., Douce, R., Marion, D., Gans, P.

Assembly

methylamine loaded form of the Glycine Cleavage System H-protein

Entity

1. Glycine Cleavage System H-protein (polymer), 131 monomers, 13947.34 Da Detail

SNVLDGLKYA PSHEWVKHEG SVATIGITDH AQDHLGEVVF VELPEPGVSV TKGKGFGAVE SVKATSDVNS PISGEVIEVN TGLTGKPGLI NSSPYEDGWM IKIKPTSPDE LESLLGAKEY TKFCEEEDAA H

2. S-aminomethyldihydrolipoate (non-polymer), 1 monomers, na Da

Formula weight

13947.34 Da

Entity Connection

amide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	amide	sing	1:LYS63:NZ	2:S-AMDHP1:CO

Source organism

Pisum sativum

Exptl. method

NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 88.3 %, Completeness (bb): 85.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	88.3 % (1274 of 1443)	95.3 % (706 of 741)	76.7 % (439 of 572)	99.2 % (129 of 130)
Backbone	85.2 % (656 of 770)	99.3 % (266 of 268)	70.4 % (267 of 379)	100.0 % (123 of 123)
Sidechain	92.4 % (730 of 790)	93.0 % (440 of 473)	91.6 % (284 of 310)	85.7 % (6 of 7)
Aromatic	79.6 % (78 of 98)	83.7 % (41 of 49)	76.6 % (36 of 47)	50.0 % (1 of 2)
Methyl	96.6 % (143 of 148)	95.9 % (71 of 74)	97.3 % (72 of 74)

1. Glycine Cleavage System H-protein

SNVLDGLKYA PSHEWVKHEG SVATIGITDH AQDHLGEVVF VELPEPGVSV TKGKGFGAVE SVKATSDVNS PISGEVIEVN TGLTGKPGLI NSSPYEDGWM IKIKPTSPDE LESLLGAKEY TKFCEEEDAA H

Show sample condition

Sample #1

Temperature 291 (±1) K, pH 5.5 (±0.1)

#	Name	Isotope labeling	Concentration
1	Glycine Cleavage System H-protein	[U-99% 15N]	2.0 mM
2	potassium phosphate		50 mM
3	EDTA		0.1 mM
4	NaN3		0.2 %
5	D2O		10 %
6	H2O		90 %

Sample #2

Temperature 291 (±1) K, pH 5.5 (±0.1)

#	Name	Isotope labeling	Concentration
7	Glycine Cleavage System H-protein	[U-99% 13C; U-99% 15N]	2.0 mM
8	potassium phosphate		50 mM
9	EDTA		0.1 mM
10	NaN3		0.2 %
11	D2O		10 %
12	H2O		90 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
¹H	H2O	protons	4.8483 ppm	internal	direct	0.0
¹⁵N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

Referencing offset: -0.13 ppm, Outliers: 3 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
¹H	H2O	protons	4.8483 ppm	internal	direct	0.0
¹⁵N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

Referencing offset: -0.13 ppm, Outliers: 3 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
¹H	H2O	protons	4.8483 ppm	internal	direct	0.0
¹⁵N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

Referencing offset: -0.06 ppm, Outliers: 2 Detail

Release date

1999-05-10

Citation 1

Backbone and sequence-specific assignment of three forms of the lipoate-containing H-protein of the glycine decarboxylase complex
Guilhaudis, L., Simorre, J., Bouchayer, E., Neuburger, M., Bourguignon, J., Douce, R., Marion, D., Gans, P.
J. Biomol. NMR (1999), 15, 185-186, PubMed 10605092 , DOI: , Abstract

Show more 1 citaion

Citation 2

1H, 13C and 15N chemical shift referencing in biomolecular NMR
Wishart, D.S., Bigam, C.G., Yao, J., Abildgaard, F., Dyson, H.J., Oldfield, E., Markley, J.L., Sykes, B.D.
J. Biomol. NMR (1995), 6, 135-140, PubMed 8589602 , DOI: , Abstract

Hide non-primary 1 citaion

Related entities 1. Glycine Cleavage System H-protein, : 1 : 3 : 161 entities Detail

Interaction partners 1. Glycine Cleavage System H-protein, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 7 experiments Detail

1 3D 1H-15N NOESY-HSQC

Instrument

#1 Model Bruker AMX (600 MHz)

#2 Model Varian INOVA (400 MHz)

#3 Model Varian INOVA (600 MHz)

Sample #1

Temperature 291 (±1) K, pH 5.5 (±0.1)

#	Name	Isotope labeling	Concentration
1	Glycine Cleavage System H-protein	[U-99% 15N]	2.0 mM
2	potassium phosphate		50 mM
3	EDTA		0.1 mM
4	NaN3		0.2 %
5	D2O		10 %
6	H2O		90 %

Sample #2

Temperature 291 (±1) K, pH 5.5 (±0.1)

#	Name	Isotope labeling	Concentration
7	Glycine Cleavage System H-protein	[U-99% 13C; U-99% 15N]	2.0 mM
8	potassium phosphate		50 mM
9	EDTA		0.1 mM
10	NaN3		0.2 %
11	D2O		10 %
12	H2O		90 %

2 3D 1H-15N TOCSY-HSQC

Instrument

#1 Model Bruker AMX (600 MHz)

#2 Model Varian INOVA (400 MHz)

#3 Model Varian INOVA (600 MHz)

Sample #1

Temperature 291 (±1) K, pH 5.5 (±0.1)

#	Name	Isotope labeling	Concentration
1	Glycine Cleavage System H-protein	[U-99% 15N]	2.0 mM
2	potassium phosphate		50 mM
3	EDTA		0.1 mM
4	NaN3		0.2 %
5	D2O		10 %
6	H2O		90 %

Sample #2

Temperature 291 (±1) K, pH 5.5 (±0.1)

#	Name	Isotope labeling	Concentration
7	Glycine Cleavage System H-protein	[U-99% 13C; U-99% 15N]	2.0 mM
8	potassium phosphate		50 mM
9	EDTA		0.1 mM
10	NaN3		0.2 %
11	D2O		10 %
12	H2O		90 %

3 3D HNCA

Instrument

#1 Model Bruker AMX (600 MHz)

#2 Model Varian INOVA (400 MHz)

#3 Model Varian INOVA (600 MHz)

Sample #1

Temperature 291 (±1) K, pH 5.5 (±0.1)

#	Name	Isotope labeling	Concentration
1	Glycine Cleavage System H-protein	[U-99% 15N]	2.0 mM
2	potassium phosphate		50 mM
3	EDTA		0.1 mM
4	NaN3		0.2 %
5	D2O		10 %
6	H2O		90 %

Sample #2

Temperature 291 (±1) K, pH 5.5 (±0.1)

#	Name	Isotope labeling	Concentration
7	Glycine Cleavage System H-protein	[U-99% 13C; U-99% 15N]	2.0 mM
8	potassium phosphate		50 mM
9	EDTA		0.1 mM
10	NaN3		0.2 %
11	D2O		10 %
12	H2O		90 %

4 3D HCCH-TOCSY

Instrument

#1 Model Bruker AMX (600 MHz)

#2 Model Varian INOVA (400 MHz)

#3 Model Varian INOVA (600 MHz)

Sample #1

Temperature 291 (±1) K, pH 5.5 (±0.1)

#	Name	Isotope labeling	Concentration
1	Glycine Cleavage System H-protein	[U-99% 15N]	2.0 mM
2	potassium phosphate		50 mM
3	EDTA		0.1 mM
4	NaN3		0.2 %
5	D2O		10 %
6	H2O		90 %

Sample #2

Temperature 291 (±1) K, pH 5.5 (±0.1)

#	Name	Isotope labeling	Concentration
7	Glycine Cleavage System H-protein	[U-99% 13C; U-99% 15N]	2.0 mM
8	potassium phosphate		50 mM
9	EDTA		0.1 mM
10	NaN3		0.2 %
11	D2O		10 %
12	H2O		90 %

5 2D 1H-15N HSQC

Instrument

#1 Model Bruker AMX (600 MHz)

#2 Model Varian INOVA (400 MHz)

#3 Model Varian INOVA (600 MHz)

Sample #1

Temperature 291 (±1) K, pH 5.5 (±0.1)

#	Name	Isotope labeling	Concentration
1	Glycine Cleavage System H-protein	[U-99% 15N]	2.0 mM
2	potassium phosphate		50 mM
3	EDTA		0.1 mM
4	NaN3		0.2 %
5	D2O		10 %
6	H2O		90 %

Sample #2

Temperature 291 (±1) K, pH 5.5 (±0.1)

#	Name	Isotope labeling	Concentration
7	Glycine Cleavage System H-protein	[U-99% 13C; U-99% 15N]	2.0 mM
8	potassium phosphate		50 mM
9	EDTA		0.1 mM
10	NaN3		0.2 %
11	D2O		10 %
12	H2O		90 %

6 2D 1H-13C HSQC

Instrument

#1 Model Bruker AMX (600 MHz)

#2 Model Varian INOVA (400 MHz)

#3 Model Varian INOVA (600 MHz)

Sample #1

Temperature 291 (±1) K, pH 5.5 (±0.1)

#	Name	Isotope labeling	Concentration
1	Glycine Cleavage System H-protein	[U-99% 15N]	2.0 mM
2	potassium phosphate		50 mM
3	EDTA		0.1 mM
4	NaN3		0.2 %
5	D2O		10 %
6	H2O		90 %

Sample #2

Temperature 291 (±1) K, pH 5.5 (±0.1)

#	Name	Isotope labeling	Concentration
7	Glycine Cleavage System H-protein	[U-99% 13C; U-99% 15N]	2.0 mM
8	potassium phosphate		50 mM
9	EDTA		0.1 mM
10	NaN3		0.2 %
11	D2O		10 %
12	H2O		90 %

7 2D 1H-1H NOESY

Instrument

#1 Model Bruker AMX (600 MHz)

#2 Model Varian INOVA (400 MHz)

#3 Model Varian INOVA (600 MHz)

Sample #1

Temperature 291 (±1) K, pH 5.5 (±0.1)

#	Name	Isotope labeling	Concentration
1	Glycine Cleavage System H-protein	[U-99% 15N]	2.0 mM
2	potassium phosphate		50 mM
3	EDTA		0.1 mM
4	NaN3		0.2 %
5	D2O		10 %
6	H2O		90 %

Sample #2

Temperature 291 (±1) K, pH 5.5 (±0.1)

#	Name	Isotope labeling	Concentration
7	Glycine Cleavage System H-protein	[U-99% 13C; U-99% 15N]	2.0 mM
8	potassium phosphate		50 mM
9	EDTA		0.1 mM
10	NaN3		0.2 %
11	D2O		10 %
12	H2O		90 %

Chemical shift validation 4 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr4336_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	True (see coodinates for details)
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

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

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:63:LYS:NZ	2:1:S-AMDHP:CO	unknown	unknown	n/a

Non-standard residues

None

Content subtype: bmr4336_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts	Warning	1382		100.0 (chain: 1, length: 131)
1	Chemical shift references	chemical_shift_reference	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 131, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 840
  - ¹³C chemical shifts: 413
  - ¹⁵N chemical shifts: 129
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- Rotameric state of ILE , LEU, and VAL
- 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 (%)
¹H chemical shifts	741	700	94.5
¹³C chemical shifts	572	413	72.2
¹⁵N chemical shifts	130	129	99.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	268	266	99.3
¹³C chemical shifts	262	131	50.0
¹⁵N chemical shifts	123	123	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	473	434	91.8
¹³C chemical shifts	310	282	91.0
¹⁵N chemical shifts	7	6	85.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	75	70	93.3
¹³C chemical shifts	75	71	94.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	49	36	73.5
¹³C chemical shifts	47	35	74.5
¹⁵N chemical shifts	2	1	50.0

Keywords Glycine decarboxylase complex, H-protein, lipoate containing protein, NMR

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 (1.305 seconds)

BMRB: 4336

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Glycine Cleavage System H-protein, : 1 : 3 : 161 entities Detail

Interaction partners 1. Glycine Cleavage System H-protein, : 1 interactors Detail

Experiments performed 7 experiments Detail

Instrument

Sample #1

Sample #2

Instrument

Sample #1

Sample #2

Instrument

Sample #1

Sample #2

Instrument

Sample #1

Sample #2

Instrument

Sample #1

Sample #2

Instrument

Sample #1

Sample #2

Instrument

Sample #1

Sample #2

Chemical shift validation 4 contents Detail