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Found 1 Document (0.641 seconds)

BMRB: 17021

2KZW

Solution NMR Structure of Q8PSA4 from Methanosarcina mazei, Northeast Structural Genomics Consortium Target MaR143A

Authors

Mills, J.L., Eletsky, A., Lee, H., Lee, D., Ciccosanti, C., Hamilton, K., Acton, T.B., Xiao, R., Everett, J.K., Prestegard, J.H., Montelione, G.T., Szyperski, T.

Assembly

MaR143A

Entity

1. MaR143A (polymer, Thiol state: not present), 145 monomers, 16255.29 Da Detail

MNARDNKFNT WNDSRGNYWS DYEGSDENGD GIGDSAYAVN PEAGSMDYMP LMEYLHSSPV LPTARFTSDI TEGFAPLSVR FKDFSENATS RLWMFGDGNT SDSPSPLHTF FNEGEYIVSL IVSNENDSDS ASVTIRALEH HHHHH

Formula weight

16255.29 Da

Source organism

Methanosarcina mazei

Exptl. method

solution NMR

Refine. method

simulated annealing, molecular dynamics

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 85.5 %, Completeness: 74.9 %, Completeness (bb): 83.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	74.9 % (1206 of 1610)	74.6 % (616 of 826)	74.0 % (467 of 631)	80.4 % (123 of 153)
Backbone	83.4 % (714 of 856)	82.6 % (242 of 293)	84.5 % (359 of 425)	81.9 % (113 of 138)
Sidechain	67.3 % (598 of 889)	69.4 % (370 of 533)	63.9 % (218 of 341)	66.7 % (10 of 15)
Aromatic	45.4 % (89 of 196)	55.1 % (54 of 98)	33.7 % (32 of 95)	100.0 % (3 of 3)
Methyl	85.5 % (94 of 110)	89.1 % (49 of 55)	81.8 % (45 of 55)

1. MaR143A

MNARDNKFNT WNDSRGNYWS DYEGSDENGD GIGDSAYAVN PEAGSMDYMP LMEYLHSSPV LPTARFTSDI TEGFAPLSVR FKDFSENATS RLWMFGDGNT SDSPSPLHTF FNEGEYIVSL IVSNENDSDS ASVTIRALEH HHHHH

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 null, Temperature 298 K, pH 7.5, Details 0.55 mM [U-100% 13C; U-100% 15N] MaR143A, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	MaR143A	[U-100% 13C; U-100% 15N]	0.55 mM
2	sodium chloride	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	sodium azide	natural abundance	0.02 %
5	TRIS	natural abundance	10 mM
6	H2O	natural abundance	95 %
7	D2O	natural abundance	5 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 null, Temperature 298 K, pH 7.5, Details 0.55 mM [U-5% 13C; U-100% 15N] MaR143A, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
8	MaR143A	[U-5% 13C; U-100% 15N]	0.55 mM
9	sodium chloride	natural abundance	100 mM
10	DTT	natural abundance	5 mM
11	sodium azide	natural abundance	0.02 %
12	TRIS	natural abundance	10 mM
13	H2O	natural abundance	95 %
14	D2O	natural abundance	5 %

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 null, Temperature 298 K, pH 7.5, Details 0.55 mM [U-5% 13C; U-100% 15N] MaR143A, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
15	MaR143A	[U-5% 13C; U-100% 15N]	0.55 mM
16	sodium chloride	natural abundance	100 mM
17	DTT	natural abundance	5 mM
18	sodium azide	natural abundance	0.02 %
19	TRIS	natural abundance	10 mM
20	Pf1 phage	natural abundance	13 mg/mL
21	H2O	natural abundance	95 %
22	D2O	natural abundance	5 %

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: 0.03 ppm, Outliers: 3 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: 0.03 ppm, Outliers: 3 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: 0.0 ppm, Outliers: 1 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: 0.53 ppm, Outliers: 3 Detail

Protein Blocks Logo

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

Release date

2010-07-25

Related entities 1. MaR143A, : 1 entities Detail

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 null, Temperature 298 K, pH 7.5, Details 0.55 mM [U-100% 13C; U-100% 15N] MaR143A, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	MaR143A	[U-100% 13C; U-100% 15N]	0.55 mM
2	sodium chloride	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	sodium azide	natural abundance	0.02 %
5	TRIS	natural abundance	10 mM
6	H2O	natural abundance	95 %
7	D2O	natural abundance	5 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 null, Temperature 298 K, pH 7.5, Details 0.55 mM [U-100% 13C; U-100% 15N] MaR143A, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	MaR143A	[U-100% 13C; U-100% 15N]	0.55 mM
2	sodium chloride	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	sodium azide	natural abundance	0.02 %
5	TRIS	natural abundance	10 mM
6	H2O	natural abundance	95 %
7	D2O	natural abundance	5 %

3 3D HNCO

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 null, Temperature 298 K, pH 7.5, Details 0.55 mM [U-100% 13C; U-100% 15N] MaR143A, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	MaR143A	[U-100% 13C; U-100% 15N]	0.55 mM
2	sodium chloride	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	sodium azide	natural abundance	0.02 %
5	TRIS	natural abundance	10 mM
6	H2O	natural abundance	95 %
7	D2O	natural abundance	5 %

4 3D CBCA(CO)NH

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 null, Temperature 298 K, pH 7.5, Details 0.55 mM [U-100% 13C; U-100% 15N] MaR143A, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	MaR143A	[U-100% 13C; U-100% 15N]	0.55 mM
2	sodium chloride	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	sodium azide	natural abundance	0.02 %
5	TRIS	natural abundance	10 mM
6	H2O	natural abundance	95 %
7	D2O	natural abundance	5 %

5 3D HNCACB

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 null, Temperature 298 K, pH 7.5, Details 0.55 mM [U-100% 13C; U-100% 15N] MaR143A, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	MaR143A	[U-100% 13C; U-100% 15N]	0.55 mM
2	sodium chloride	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	sodium azide	natural abundance	0.02 %
5	TRIS	natural abundance	10 mM
6	H2O	natural abundance	95 %
7	D2O	natural abundance	5 %

6 3D HBHA(CO)NH

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 null, Temperature 298 K, pH 7.5, Details 0.55 mM [U-100% 13C; U-100% 15N] MaR143A, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	MaR143A	[U-100% 13C; U-100% 15N]	0.55 mM
2	sodium chloride	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	sodium azide	natural abundance	0.02 %
5	TRIS	natural abundance	10 mM
6	H2O	natural abundance	95 %
7	D2O	natural abundance	5 %

7 3D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 null, Temperature 298 K, pH 7.5, Details 0.55 mM [U-100% 13C; U-100% 15N] MaR143A, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	MaR143A	[U-100% 13C; U-100% 15N]	0.55 mM
2	sodium chloride	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	sodium azide	natural abundance	0.02 %
5	TRIS	natural abundance	10 mM
6	H2O	natural abundance	95 %
7	D2O	natural abundance	5 %

8 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State anisotropic, Solvent system 95% H2O/5% D2O, Pressure 1 null, Temperature 298 K, pH 7.5, Details 0.55 mM [U-5% 13C; U-100% 15N] MaR143A, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
15	MaR143A	[U-5% 13C; U-100% 15N]	0.55 mM
16	sodium chloride	natural abundance	100 mM
17	DTT	natural abundance	5 mM
18	sodium azide	natural abundance	0.02 %
19	TRIS	natural abundance	10 mM
20	Pf1 phage	natural abundance	13 mg/mL
21	H2O	natural abundance	95 %
22	D2O	natural abundance	5 %

9 2D 1H-13C HSQC

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 null, Temperature 298 K, pH 7.5, Details 0.55 mM [U-5% 13C; U-100% 15N] MaR143A, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
8	MaR143A	[U-5% 13C; U-100% 15N]	0.55 mM
9	sodium chloride	natural abundance	100 mM
10	DTT	natural abundance	5 mM
11	sodium azide	natural abundance	0.02 %
12	TRIS	natural abundance	10 mM
13	H2O	natural abundance	95 %
14	D2O	natural abundance	5 %

10 3D HCCH-TOCSY

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 null, Temperature 298 K, pH 7.5, Details 0.55 mM [U-100% 13C; U-100% 15N] MaR143A, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	MaR143A	[U-100% 13C; U-100% 15N]	0.55 mM
2	sodium chloride	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	sodium azide	natural abundance	0.02 %
5	TRIS	natural abundance	10 mM
6	H2O	natural abundance	95 %
7	D2O	natural abundance	5 %

11 3D HCCH-COSY

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 null, Temperature 298 K, pH 7.5, Details 0.55 mM [U-100% 13C; U-100% 15N] MaR143A, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	MaR143A	[U-100% 13C; U-100% 15N]	0.55 mM
2	sodium chloride	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	sodium azide	natural abundance	0.02 %
5	TRIS	natural abundance	10 mM
6	H2O	natural abundance	95 %
7	D2O	natural abundance	5 %

12 HB(CBCGCDCE)HE

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 null, Temperature 298 K, pH 7.5, Details 0.55 mM [U-100% 13C; U-100% 15N] MaR143A, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	MaR143A	[U-100% 13C; U-100% 15N]	0.55 mM
2	sodium chloride	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	sodium azide	natural abundance	0.02 %
5	TRIS	natural abundance	10 mM
6	H2O	natural abundance	95 %
7	D2O	natural abundance	5 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_17021_2kzw.nef
Input source #2: Coordindates	2kzw.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--------80--------90-------100
MNARDNKFNTWNDSRGNYWSDYEGSDENGDGIGDSAYAVNPEAGSMDYMPLMEYLHSSPVLPTARFTSDITEGFAPLSVRFKDFSENATSRLWMFGDGNT
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MNARDNKFNTWNDSRGNYWSDYEGSDENGDGIGDSAYAVNPEAGSMDYMPLMEYLHSSPVLPTARFTSDITEGFAPLSVRFKDFSENATSRLWMFGDGNT

-------110-------120-------130-------140-----
SDSPSPLHTFFNEGEYIVSLIVSNENDSDSASVTIRALEHHHHHH
|||||||||||||||||||||||||||||||||||||||||||||
SDSPSPLHTFFNEGEYIVSLIVSNENDSDSASVTIRALEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	145	0	0	100.0

Content subtype: combined_17021_2kzw.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1189		84.8 (chain: A, length: 145)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1636 (1)	noe	81.4 (chain: A, length: 145)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	124 (124)	.	54.5 (chain: A, length: 145)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_4	OK	60 (60)	.	40.7 (chain: A, length: 145)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 145, Sequence coverage: 84.8%
- Total number of assignments
  - ¹H chemical shifts: 608
  - ¹³C chemical shifts: 460
  - ¹⁵N chemical shifts: 121
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- 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)
67	THR	HG1	5.264
85	SER	HG	6.825
100	THR	HG1	6.187

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	826	605	73.2
¹³C chemical shifts	631	460	72.9
¹⁵N chemical shifts	159	121	76.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	293	243	82.9
¹³C chemical shifts	290	245	84.5
¹⁵N chemical shifts	138	112	81.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	533	362	67.9
¹³C chemical shifts	341	215	63.0
¹⁵N chemical shifts	21	9	42.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	60	49	81.7
¹³C chemical shifts	60	45	75.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	98	49	50.0
¹³C chemical shifts	95	29	30.5
¹⁵N chemical shifts	3	3	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: 145, Sequence coverage: 81.4%
- Total number of restraints: 1633
- Weight of restraints: 1.0 (1633)
- Potential type of restraints: square-well-parabolic (1633)
- Range of distance target values: 1.41, 3.15 (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

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 145, Sequence coverage: 54.5%
- Total number of restraints: 124
- Total number of restraints per polymer type: 124
- Weight of restraints: 1.0 (124)
- Potential type of restraints: square-well-parabolic (124)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 145, Sequence coverage: 40.7%
- Total number of restraints: 60
- Potential type of restraints: undefined (60)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue

Keywords NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG), PSI-2, Protein NMR, Protein Structure Initiative, Structural Genomics, Target MaR143A

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Found 1 Document (0.641 seconds)

BMRB: 17021

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. MaR143A, : 1 entities Detail

Experiments performed 12 experiments Detail

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NMR combined restraints 5 contents Detail