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BMRB: 15339

2JRM

Solution NMR Structure of Ribosome Modulation Factor VP1593 from Vibrio parahaemolyticus. Northeast Structural Genomics Target VpR55

Authors

Tang, Y., Rossi, P., Swapna, G., Wang, H., Jiang, M., Cunningham, K., Owens, L., Ma, L., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T.

Assembly

Ribosome Modulation Factor

Entity

1. Ribosome Modulation Factor (polymer, Thiol state: all free), 65 monomers, 7786.499 Da Detail

MKRQKRDRLE RAQSQGYKAG LNGRSQEACP YQQVDARSYW LGGWRDARDE KQSGLYKLEH HHHHH

Formula weight

7786.499 Da

Source organism

Vibrio parahaemolyticus

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 92.3 %, Completeness: 89.3 %, Completeness (bb): 90.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.3 % (699 of 783)	89.0 % (373 of 419)	89.0 % (258 of 290)	91.9 % (68 of 74)
Backbone	90.7 % (352 of 388)	91.1 % (123 of 135)	90.5 % (171 of 189)	90.6 % (58 of 64)
Sidechain	88.1 % (400 of 454)	88.0 % (250 of 284)	87.5 % (140 of 160)	100.0 % (10 of 10)
Aromatic	70.0 % (56 of 80)	70.0 % (28 of 40)	68.4 % (26 of 38)	100.0 % (2 of 2)
Methyl	100.0 % (34 of 34)	100.0 % (17 of 17)	100.0 % (17 of 17)

1. VpR55

MKRQKRDRLE RAQSQGYKAG LNGRSQEACP YQQVDARSYW LGGWRDARDE KQSGLYKLEH HHHHH

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 393 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	VpR55	[U-100% 13C; U-100% 15N]		1.1 mM
2	MES	natural abundance		20 mM
3	NaCl	natural abundance		100 mM
4	CaCl2	natural abundance		5 mM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.02 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 393 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
7	VpR55	[U-5% 13C; U-100% 15N]		1.1 mM
8	MES	natural abundance		20 mM
9	NaCl	natural abundance		100 mM
10	CaCl2	natural abundance		5 mM
11	DTT	natural abundance		10 mM
12	NaN3	natural abundance		0.02 %

LACS Plot; CA

Referencing offset: -0.13 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: -0.13 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: 0.05 ppm, Outliers: 2 Detail

LACS Plot; CO

Referencing offset: -0.3 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2007-07-26

Citation

Solution NMR Structure of Ribosome Modulation Factor VP1593 from Vibrio parahaemolyticus
Tang, Y., Rossi, P., Swapna, G., Wang, H., Jiang, M., Cunningham, K., Owens, L., Ma, L., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T.
Not known

Related entities 1. Ribosome Modulation Factor, : 1 : 21 entities Detail

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 393 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	VpR55	[U-100% 13C; U-100% 15N]		1.1 mM
2	MES	natural abundance		20 mM
3	NaCl	natural abundance		100 mM
4	CaCl2	natural abundance		5 mM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.02 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 393 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	VpR55	[U-100% 13C; U-100% 15N]		1.1 mM
2	MES	natural abundance		20 mM
3	NaCl	natural abundance		100 mM
4	CaCl2	natural abundance		5 mM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.02 %

3 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 393 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	VpR55	[U-100% 13C; U-100% 15N]		1.1 mM
2	MES	natural abundance		20 mM
3	NaCl	natural abundance		100 mM
4	CaCl2	natural abundance		5 mM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.02 %

4 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 393 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	VpR55	[U-100% 13C; U-100% 15N]		1.1 mM
2	MES	natural abundance		20 mM
3	NaCl	natural abundance		100 mM
4	CaCl2	natural abundance		5 mM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.02 %

5 3D 1H-13C NOESY_aromatic

Instrument

Bruker Avance - 800 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 393 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	VpR55	[U-100% 13C; U-100% 15N]		1.1 mM
2	MES	natural abundance		20 mM
3	NaCl	natural abundance		100 mM
4	CaCl2	natural abundance		5 mM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.02 %

6 3D HNCO

Instrument

Bruker Avance - 800 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 393 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	VpR55	[U-100% 13C; U-100% 15N]		1.1 mM
2	MES	natural abundance		20 mM
3	NaCl	natural abundance		100 mM
4	CaCl2	natural abundance		5 mM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.02 %

7 3D HNCACB

Instrument

Bruker Avance - 800 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 393 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	VpR55	[U-100% 13C; U-100% 15N]		1.1 mM
2	MES	natural abundance		20 mM
3	NaCl	natural abundance		100 mM
4	CaCl2	natural abundance		5 mM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.02 %

8 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 393 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	VpR55	[U-100% 13C; U-100% 15N]		1.1 mM
2	MES	natural abundance		20 mM
3	NaCl	natural abundance		100 mM
4	CaCl2	natural abundance		5 mM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.02 %

9 3D HBHA(CO)NH

Instrument

Bruker Avance - 800 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 393 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	VpR55	[U-100% 13C; U-100% 15N]		1.1 mM
2	MES	natural abundance		20 mM
3	NaCl	natural abundance		100 mM
4	CaCl2	natural abundance		5 mM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.02 %

10 3D C(CO)NH

Instrument

Bruker Avance - 800 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 393 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	VpR55	[U-100% 13C; U-100% 15N]		1.1 mM
2	MES	natural abundance		20 mM
3	NaCl	natural abundance		100 mM
4	CaCl2	natural abundance		5 mM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.02 %

11 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 393 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	VpR55	[U-100% 13C; U-100% 15N]		1.1 mM
2	MES	natural abundance		20 mM
3	NaCl	natural abundance		100 mM
4	CaCl2	natural abundance		5 mM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.02 %

12 3D CCH-TOCSY

Instrument

Bruker Avance - 800 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 393 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	VpR55	[U-100% 13C; U-100% 15N]		1.1 mM
2	MES	natural abundance		20 mM
3	NaCl	natural abundance		100 mM
4	CaCl2	natural abundance		5 mM
5	DTT	natural abundance		10 mM
6	NaN3	natural abundance		0.02 %

13 2D 1H-13C HSQC_high resolution

Instrument

Bruker Avance - 800 MHz cryoprobe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 393 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
7	VpR55	[U-5% 13C; U-100% 15N]		1.1 mM
8	MES	natural abundance		20 mM
9	NaCl	natural abundance		100 mM
10	CaCl2	natural abundance		5 mM
11	DTT	natural abundance		10 mM
12	NaN3	natural abundance		0.02 %

NMR combined restraints 8 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15339_2jrm.nef
Input source #2: Coordindates	2jrm.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-----
MKRQKRDRLERAQSQGYKAGLNGRSQEACPYQQVDARSYWLGGWRDARDEKQSGLYKLEHHHHHH
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MKRQKRDRLERAQSQGYKAGLNGRSQEACPYQQVDARSYWLGGWRDARDEKQSGLYKLEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	65	0	0	100.0

Content subtype: combined_15339_2jrm.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	702		92.3 (chain: A, length: 65)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1353 (1)	noe	92.3 (chain: A, length: 65)
2	Distance restraints	CNS/XPLOR_distance_constraints_5	OK	1353 (1)	noe	92.3 (chain: A, length: 65)
3	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	50 (1)	hbond	53.8 (chain: A, length: 65)
4	Distance restraints	CNS/XPLOR_distance_constraints_7	OK	50 (1)	hbond	53.8 (chain: A, length: 65)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	154 (154)	.	75.4 (chain: A, length: 65)
2	Dihedral angle restraints	CNS/XPLOR_dihedral_6	OK	154 (154)	.	75.4 (chain: A, length: 65)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 65, Sequence coverage: 92.3%
- Total number of assignments
  - ¹H chemical shifts: 373
  - ¹³C chemical shifts: 258
  - ¹⁵N chemical shifts: 71
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 65, Sequence coverage: 92.3%
- Total number of restraints: 1352
- Weight of restraints: 1.0 (1352)
- Potential type of restraints: square-well-parabolic (1352)
- Range of distance target values: 2.35, 3.4 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_5
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 65, Sequence coverage: 92.3%
  - Total number of restraints: 1352
  - Weight of restraints: 1.0 (1352)
  - Potential type of restraints: square-well-parabolic (1352)
  - Range of distance target values: 2.35, 3.4 (Å)
  - Histogram of 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: 65, Sequence coverage: 53.8%
    - Total number of restraints: 50
    - Weight of restraints: 1.0 (50)
    - Potential type of restraints: square-well-parabolic (50)
    - Range of distance target values: 1.9, 2.85 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map
    - Saveframe: CNS/XPLOR_distance_constraints_7
      - Status: OK
      - Experiment type: hbond
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 65, Sequence coverage: 53.8%
        --------10--------20--------30--------40--------50--------60----- MKRQKRDRLERAQSQGYKAGLNGRSQEACPYQQVDARSYWLGGWRDARDEKQSGLYKLEHHHHHH ||| |||||| ||| || ||||||||||||||||||||| ......DRL.RAQSQG.KAG.NG.........QVDARSYWLGGWRDARDEKQS --------10--------20--------30--------40--------50---
      - Total number of restraints: 50
        Total hydrogen bond restraints: 50
        O...h-N: 25
        O...H-x: 25
      - Weight of restraints: 1.0 (50)
        Total hydrogen bond restraints: 1.0 (50)
        O...h-N: 1.0 (25)
        O...H-x: 1.0 (25)
      - Potential type of restraints: square-well-parabolic (50)
        Total hydrogen bond restraints: square-well-parabolic (50)
        O...h-N: square-well-parabolic (25)
        O...H-x: square-well-parabolic (25)
      - Range of distance target values: 1.9, 2.85 (Å)
      - Histogram of distance target values
      - Distance restraints per residue
        Chain_ID: A
      - Distance restraints on contact map
        Chain_ID_1: A - Chain_ID_2: A

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 65, Sequence coverage: 75.4%
- Total number of restraints: 154
- Total number of restraints per polymer type: 154
- Weight of restraints: 1.0 (154)
- Potential type of restraints: square-well-parabolic (154)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
- Saveframe: CNS/XPLOR_dihedral_6
  - Status: OK
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 65, Sequence coverage: 75.4%
  - Total number of restraints: 154
  - Total number of restraints per polymer type: 154
  - Weight of restraints: 1.0 (154)
  - Potential type of restraints: square-well-parabolic (154)
  - Plot of Phi-Psi angle restraints
  - Dihedral angle restraints per residue
    - Chain_ID: A

Keywords solution NMR structure