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Found 1 Document (0.816 seconds)

BMRB: 15702

2K2E

Solution NMR Structure of Bordatella pertussis protein BP2786, a Mth938-like domain: Northeast Structural Genomics Consortium target BeR31

Authors

Cort, J.R., Ho, C.K., Nwosu, C., Maglaqui, M., Xiao, R., Liu, J., Baran, M.C., Swapna, G., Acton, T.B., Rost, B., Montelione, G.T., Kennedy, M.A.

Assembly

BP2786

Entity

1. BP2786 (polymer, Thiol state: all free), 158 monomers, 16853.89 Da Detail

MKLHTDPATA LNTVTAYGDG YIEVNQVRFS HAIAFAPEGP VASWPVQRPA DITASLLQQA AGLAEVVRDP LAFLDEPEAG AGARPANAPE VLLVGTGRRQ HLLGPEQVRP LLAMGVGVEA MDTQAAARTY NILMAEGRRV VVALLPDGDS LEHHHHHH

Formula weight

16853.89 Da

Source organism

Bordetella pertussis

Exptl. method

solution NMR

Refine. method

molecular dynamics, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.3 %, Completeness: 77.1 %, Completeness (bb): 89.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	77.1 % (1330 of 1725)	73.8 % (652 of 883)	79.2 % (542 of 684)	86.1 % (136 of 158)
Backbone	89.3 % (825 of 924)	87.7 % (278 of 317)	89.6 % (413 of 461)	91.8 % (134 of 146)
Sidechain	67.5 % (639 of 946)	66.1 % (374 of 566)	71.5 % (263 of 368)	16.7 % (2 of 12)
Aromatic	32.4 % (33 of 102)	35.3 % (18 of 51)	28.0 % (14 of 50)	100.0 % (1 of 1)
Methyl	83.8 % (176 of 210)	83.8 % (88 of 105)	83.8 % (88 of 105)

1. BP2786

MKLHTDPATA LNTVTAYGDG YIEVNQVRFS HAIAFAPEGP VASWPVQRPA DITASLLQQA AGLAEVVRDP LAFLDEPEAG AGARPANAPE VLLVGTGRRQ HLLGPEQVRP LLAMGVGVEA MDTQAAARTY NILMAEGRRV VVALLPDGDS LEHHHHHH

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	BP2786		0.0 ~ 0.0 mM
2	sodium chloride	natural abundance	100 mM
3	MES	natural abundance	20 mM
4	DTT	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	calcium chloride	natural abundance	5 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
7	BP2786		0.0 ~ 0.0 mM
8	sodium chloride	natural abundance	100 mM
9	MES	natural abundance	20 mM
10	DTT	natural abundance	10 mM
11	sodium azide	natural abundance	0.02 %
12	calcium chloride	natural abundance	5 mM

LACS Plot; CA

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

Referencing offset: -0.05 ppm, Outliers: 2 Detail

LACS Plot; CB

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

Referencing offset: -0.05 ppm, Outliers: 2 Detail

LACS Plot; HA

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

Referencing offset: 0.03 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: 0.58 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2K2E, Strand ID: A Detail

Release date

2009-10-11

Citation

Solution structure of Bordatella pertussis protein BP2786
Cort, J.R., Kennedy, M.A.
Not known

Related entities 1. BP2786, : 1 : 1 : 5 entities Detail

Experiments performed 13 experiments Detail

1 3D 1H-13C NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	BP2786		0.0 ~ 0.0 mM
2	sodium chloride	natural abundance	100 mM
3	MES	natural abundance	20 mM
4	DTT	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	calcium chloride	natural abundance	5 mM

2 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	BP2786		0.0 ~ 0.0 mM
2	sodium chloride	natural abundance	100 mM
3	MES	natural abundance	20 mM
4	DTT	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	calcium chloride	natural abundance	5 mM

3 4D 1H-13C-13C-1H HMQC-NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
7	BP2786		0.0 ~ 0.0 mM
8	sodium chloride	natural abundance	100 mM
9	MES	natural abundance	20 mM
10	DTT	natural abundance	10 mM
11	sodium azide	natural abundance	0.02 %
12	calcium chloride	natural abundance	5 mM

4 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	BP2786		0.0 ~ 0.0 mM
2	sodium chloride	natural abundance	100 mM
3	MES	natural abundance	20 mM
4	DTT	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	calcium chloride	natural abundance	5 mM

5 3D HCCH-COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	BP2786		0.0 ~ 0.0 mM
2	sodium chloride	natural abundance	100 mM
3	MES	natural abundance	20 mM
4	DTT	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	calcium chloride	natural abundance	5 mM

6 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	BP2786		0.0 ~ 0.0 mM
2	sodium chloride	natural abundance	100 mM
3	MES	natural abundance	20 mM
4	DTT	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	calcium chloride	natural abundance	5 mM

7 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	BP2786		0.0 ~ 0.0 mM
2	sodium chloride	natural abundance	100 mM
3	MES	natural abundance	20 mM
4	DTT	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	calcium chloride	natural abundance	5 mM

8 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	BP2786		0.0 ~ 0.0 mM
2	sodium chloride	natural abundance	100 mM
3	MES	natural abundance	20 mM
4	DTT	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	calcium chloride	natural abundance	5 mM

9 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	BP2786		0.0 ~ 0.0 mM
2	sodium chloride	natural abundance	100 mM
3	MES	natural abundance	20 mM
4	DTT	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	calcium chloride	natural abundance	5 mM

10 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	BP2786		0.0 ~ 0.0 mM
2	sodium chloride	natural abundance	100 mM
3	MES	natural abundance	20 mM
4	DTT	natural abundance	10 mM
5	sodium azide	natural abundance	0.02 %
6	calcium chloride	natural abundance	5 mM

11 3D 1H-13C NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
7	BP2786		0.0 ~ 0.0 mM
8	sodium chloride	natural abundance	100 mM
9	MES	natural abundance	20 mM
10	DTT	natural abundance	10 mM
11	sodium azide	natural abundance	0.02 %
12	calcium chloride	natural abundance	5 mM

12 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
7	BP2786		0.0 ~ 0.0 mM
8	sodium chloride	natural abundance	100 mM
9	MES	natural abundance	20 mM
10	DTT	natural abundance	10 mM
11	sodium azide	natural abundance	0.02 %
12	calcium chloride	natural abundance	5 mM

13 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
7	BP2786		0.0 ~ 0.0 mM
8	sodium chloride	natural abundance	100 mM
9	MES	natural abundance	20 mM
10	DTT	natural abundance	10 mM
11	sodium azide	natural abundance	0.02 %
12	calcium chloride	natural abundance	5 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15702_2k2e.nef
Input source #2: Coordindates	2k2e.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
MKLHTDPATALNTVTAYGDGYIEVNQVRFSHAIAFAPEGPVASWPVQRPADITASLLQQAAGLAEVVRDPLAFLDEPEAGAGARPANAPEVLLVGTGRRQ
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MKLHTDPATALNTVTAYGDGYIEVNQVRFSHAIAFAPEGPVASWPVQRPADITASLLQQAAGLAEVVRDPLAFLDEPEAGAGARPANAPEVLLVGTGRRQ

-------110-------120-------130-------140-------150--------
HLLGPEQVRPLLAMGVGVEAMDTQAAARTYNILMAEGRRVVVALLPDGDSLEHHHHHH
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
HLLGPEQVRPLLAMGVGVEAMDTQAAARTYNILMAEGRRVVVALLPDGDSLEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	158	0	0	100.0

Content subtype: combined_15702_2k2e.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	CHEMSHIFTS	Warning	1315		92.4 (chain: A, length: 158)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	570 (1)	noe	66.5 (chain: A, length: 158)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	45 (1)	hbond	21.5 (chain: A, length: 158)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	97 (97)	.	50.6 (chain: A, length: 158)

Assigned chemical shifts

Saveframe: CHEMSHIFTS
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 158, Sequence coverage: 92.4%
- Total number of assignments
  - ¹H chemical shifts: 651
  - ¹³C chemical shifts: 532
  - ¹⁵N chemical shifts: 132
- 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)
55	SER	HG	5.66
101	HIS	HD1	6.86
123	THR	HG1	5.94

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	883	648	73.4
¹³C chemical shifts	684	532	77.8
¹⁵N chemical shifts	168	132	78.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	317	278	87.7
¹³C chemical shifts	316	275	87.0
¹⁵N chemical shifts	146	130	89.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	566	370	65.4
¹³C chemical shifts	368	257	69.8
¹⁵N chemical shifts	22	2	9.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	109	94	86.2
¹³C chemical shifts	109	94	86.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	51	18	35.3
¹³C chemical shifts	50	14	28.0
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 158, Sequence coverage: 66.5%
- Total number of restraints: 570
- Weight of restraints: 1.0 (570)
- Potential type of restraints: square-well-parabolic (570)
- Range of distance target values: 2.25, 3.65 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 158, Sequence coverage: 21.5%
  - Total number of restraints: 45
  - Weight of restraints: 1.0 (45)
  - Potential type of restraints: square-well-parabolic (45)
  - Range of distance target values: 2.0, 3.0 (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_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 158, Sequence coverage: 50.6%
- Total number of restraints: 97
- Total number of restraints per polymer type: 97
- Weight of restraints: 1.0 (97)
- Potential type of restraints: square-well-parabolic (97)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords COG03737, DUF 498, MTH938-like fold

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Found 1 Document (0.816 seconds)

BMRB: 15702

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. BP2786, : 1 : 1 : 5 entities Detail

Experiments performed 13 experiments Detail

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NMR combined restraints 5 contents Detail