BMRBj - BMREntryMaster

Found 1 Document (0.723 seconds)

BMRB: 18987

2M46

Solution NMR structure of SACOL0876 from Staphylococcus aureus COL, NESG target ZR353 and CSGID target IDP00841

Authors

Wu, B., Yee, A., Houliston, S., Garcia, M., Savchenko, A., Arrowsmith, C.H.

Assembly

SACOL0876

Entity

1. SACOL0876 (polymer, Thiol state: all free), 142 monomers, 16337.40 Da Detail

MHHHHHHSSG VDLGTENLYF QSNAMIKFYQ YKNCTTCKKA AKFLDEYGVS YEPIDIVQHT PTINEFKTII ANTGVEINKL FNTHGAKYRE LDLKNKLQTL SDDEKLELLS SDGMLVKRPL AVMGDKITLG FKEDQYKETW LA

Formula weight

16337.4 Da

Source organism

Staphylococcus aureus

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 85.2 %, Completeness: 78.3 %, Completeness (bb): 81.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	78.3 % (1335 of 1705)	79.0 % (699 of 885)	77.7 % (518 of 667)	77.1 % (118 of 153)
Backbone	81.7 % (691 of 846)	81.7 % (236 of 289)	82.1 % (343 of 418)	80.6 % (112 of 139)
Sidechain	76.1 % (756 of 993)	77.7 % (463 of 596)	74.9 % (287 of 383)	42.9 % (6 of 14)
Aromatic	51.9 % (83 of 160)	65.0 % (52 of 80)	38.0 % (30 of 79)	100.0 % (1 of 1)
Methyl	86.8 % (132 of 152)	86.8 % (66 of 76)	86.8 % (66 of 76)

1. SACOL0876

MHHHHHHSSG VDLGTENLYF QSNAMIKFYQ YKNCTTCKKA AKFLDEYGVS YEPIDIVQHT PTINEFKTII ANTGVEINKL FNTHGAKYRE LDLKNKLQTL SDDEKLELLS SDGMLVKRPL AVMGDKITLG FKEDQYKETW LA

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	SACOL0876	[U-100% 13C; U-100% 15N]	0.3 mM
2	TRIS	[U-100% 2H]	10 mM
3	sodium chloride	natural abundance	300 mM
4	DTT	[U-100% 2H]	10 mM
5	NaN3	natural abundance	0.01 %
6	benzamidine	natural abundance	10 mM
7	inhibitor cocktail	natural abundance	1 na

Sample #2

Solvent system 99% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
8	SACOL0876	[U-100% 13C; U-100% 15N]	0.3 mM
9	TRIS	[U-100% 2H]	10 mM
10	sodium chloride	natural abundance	300 mM
11	DTT	[U-100% 2H]	10 mM
12	NaN3	natural abundance	0.01 %
13	benzamidine	natural abundance	10 mM
14	inhibitor cocktail	natural abundance	1 na

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
15	SACOL0876	[U-7% 13C; U-100% 15N]	0.2 mM
16	TRIS	[U-100% 2H]	10 mM
17	sodium chloride	natural abundance	300 mM
18	DTT	[U-100% 2H]	10 mM
19	NaN3	natural abundance	0.01 %
20	benzamidine	natural abundance	10 mM
21	inhibitor cocktail	natural abundance	1 na

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: -0.3 ppm, Outliers: 2 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: -0.3 ppm, Outliers: 2 Detail

LACS Plot; HA

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: 0.12 ppm, Outliers: 2 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: 0.0 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2M46, Strand ID: A Detail

Release date

2013-01-31

Citation

Solution NMR structure of SACOL0876 from Staphylococcus aureus COL, NESG target ZR353 and CSGID target IDP00841
Wu, B., Yee, A., Houliston, S., Garcia, M., Savchenko, A., Arrowsmith, C.H.
Not known

Related entities 1. SACOL0876, : 1 : 1 : 27 entities Detail

Experiments performed 11 experiments Detail

1 3D HNCO

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	SACOL0876	[U-100% 13C; U-100% 15N]	0.3 mM
2	TRIS	[U-100% 2H]	10 mM
3	sodium chloride	natural abundance	300 mM
4	DTT	[U-100% 2H]	10 mM
5	NaN3	natural abundance	0.01 %
6	benzamidine	natural abundance	10 mM
7	inhibitor cocktail	natural abundance	1 na

2 3D CBCA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	SACOL0876	[U-100% 13C; U-100% 15N]	0.3 mM
2	TRIS	[U-100% 2H]	10 mM
3	sodium chloride	natural abundance	300 mM
4	DTT	[U-100% 2H]	10 mM
5	NaN3	natural abundance	0.01 %
6	benzamidine	natural abundance	10 mM
7	inhibitor cocktail	natural abundance	1 na

3 3D HBHA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	SACOL0876	[U-100% 13C; U-100% 15N]	0.3 mM
2	TRIS	[U-100% 2H]	10 mM
3	sodium chloride	natural abundance	300 mM
4	DTT	[U-100% 2H]	10 mM
5	NaN3	natural abundance	0.01 %
6	benzamidine	natural abundance	10 mM
7	inhibitor cocktail	natural abundance	1 na

4 3D HNCA

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	SACOL0876	[U-100% 13C; U-100% 15N]	0.3 mM
2	TRIS	[U-100% 2H]	10 mM
3	sodium chloride	natural abundance	300 mM
4	DTT	[U-100% 2H]	10 mM
5	NaN3	natural abundance	0.01 %
6	benzamidine	natural abundance	10 mM
7	inhibitor cocktail	natural abundance	1 na

5 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	SACOL0876	[U-100% 13C; U-100% 15N]	0.3 mM
2	TRIS	[U-100% 2H]	10 mM
3	sodium chloride	natural abundance	300 mM
4	DTT	[U-100% 2H]	10 mM
5	NaN3	natural abundance	0.01 %
6	benzamidine	natural abundance	10 mM
7	inhibitor cocktail	natural abundance	1 na

6 3D CCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	SACOL0876	[U-100% 13C; U-100% 15N]	0.3 mM
2	TRIS	[U-100% 2H]	10 mM
3	sodium chloride	natural abundance	300 mM
4	DTT	[U-100% 2H]	10 mM
5	NaN3	natural abundance	0.01 %
6	benzamidine	natural abundance	10 mM
7	inhibitor cocktail	natural abundance	1 na

7 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	SACOL0876	[U-100% 13C; U-100% 15N]	0.3 mM
2	TRIS	[U-100% 2H]	10 mM
3	sodium chloride	natural abundance	300 mM
4	DTT	[U-100% 2H]	10 mM
5	NaN3	natural abundance	0.01 %
6	benzamidine	natural abundance	10 mM
7	inhibitor cocktail	natural abundance	1 na

8 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	SACOL0876	[U-100% 13C; U-100% 15N]	0.3 mM
2	TRIS	[U-100% 2H]	10 mM
3	sodium chloride	natural abundance	300 mM
4	DTT	[U-100% 2H]	10 mM
5	NaN3	natural abundance	0.01 %
6	benzamidine	natural abundance	10 mM
7	inhibitor cocktail	natural abundance	1 na

9 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	SACOL0876	[U-100% 13C; U-100% 15N]	0.3 mM
2	TRIS	[U-100% 2H]	10 mM
3	sodium chloride	natural abundance	300 mM
4	DTT	[U-100% 2H]	10 mM
5	NaN3	natural abundance	0.01 %
6	benzamidine	natural abundance	10 mM
7	inhibitor cocktail	natural abundance	1 na

10 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 99% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
8	SACOL0876	[U-100% 13C; U-100% 15N]	0.3 mM
9	TRIS	[U-100% 2H]	10 mM
10	sodium chloride	natural abundance	300 mM
11	DTT	[U-100% 2H]	10 mM
12	NaN3	natural abundance	0.01 %
13	benzamidine	natural abundance	10 mM
14	inhibitor cocktail	natural abundance	1 na

11 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Concentration
15	SACOL0876	[U-7% 13C; U-100% 15N]	0.2 mM
16	TRIS	[U-100% 2H]	10 mM
17	sodium chloride	natural abundance	300 mM
18	DTT	[U-100% 2H]	10 mM
19	NaN3	natural abundance	0.01 %
20	benzamidine	natural abundance	10 mM
21	inhibitor cocktail	natural abundance	1 na

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18987_2m46.nef
Input source #2: Coordindates	2m46.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
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)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------------------------------10--------20--------30--------40--------50--------60--------70------
MHHHHHHSSGVDLGTENLYFQSNAMIKFYQYKNCTTCKKAAKFLDEYGVSYEPIDIVQHTPTINEFKTIIANTGVEINKLFNTHGAKYRELDLKNKLQTL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MHHHHHHSSGVDLGTENLYFQSNAMIKFYQYKNCTTCKKAAKFLDEYGVSYEPIDIVQHTPTINEFKTIIANTGVEINKLFNTHGAKYRELDLKNKLQTL
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

--80--------90-------100-------110--------
SDDEKLELLSSDGMLVKRPLAVMGDKITLGFKEDQYKETWLA
||||||||||||||||||||||||||||||||||||||||||
SDDEKLELLSSDGMLVKRPLAVMGDKITLGFKEDQYKETWLA
-------110-------120-------130-------140--

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	142	0	0	100.0

Content subtype: combined_18987_2m46.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1272		78.9 (chain: A, length: 142)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	3738 (1)	noe	78.2 (chain: A, length: 142)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	82 (1)	hbond	44.4 (chain: A, length: 142)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	182 (182)	.	77.5 (chain: A, length: 142)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 142, Sequence coverage: 78.9%
- Total number of assignments
  - ¹H chemical shifts: 676
  - ¹³C chemical shifts: 487
  - ¹⁵N chemical shifts: 109
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: A

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
36	THR	HG1	5.247
49	THR	HG1	4.217

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	885	674	76.2
¹³C chemical shifts	667	487	73.0
¹⁵N chemical shifts	155	109	70.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	289	219	75.8
¹³C chemical shifts	284	212	74.6
¹⁵N chemical shifts	139	103	74.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	596	455	76.3
¹³C chemical shifts	383	275	71.8
¹⁵N chemical shifts	16	6	37.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	80	67	83.8
¹³C chemical shifts	80	67	83.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	80	48	60.0
¹³C chemical shifts	79	26	32.9
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 142, Sequence coverage: 78.2%
- Total number of restraints: 3738
- Weight of restraints: 1.0 (3738)
- Potential type of restraints: square-well-parabolic (3738)
- Range of distance target values: 2.25, 3.9 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 142, Sequence coverage: 44.4%
  - Total number of restraints: 82
  - Weight of restraints: 1.0 (82)
  - Potential type of restraints: square-well-parabolic (82)
  - Range of distance target values: 1.95, 2.9 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 142, Sequence coverage: 77.5%
- Total number of restraints: 182
- Total number of restraints per polymer type: 182
- Weight of restraints: 1.0 (182)
- Potential type of restraints: square-well-parabolic (182)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords pathogenic bacterial protein

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 (0.723 seconds)

BMRB: 18987

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. SACOL0876, : 1 : 1 : 27 entities Detail

Experiments performed 11 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail