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BMRB: 15085

2JN4

Complete Assignment of a hypothetical portein RP4601 (NESG ID: RpT2)from Rhodopseudomonas palustris.

Authors

Lemak, A., Srisailam, S., Yee, A., Karra, M.D., Lukin, J.A., Arrowsmith, C.H.

Assembly

RP4601 assembly

Entity

1. RP4601 assembly (polymer, Thiol state: not present), 66 monomers, 7247.474 Da Detail

MKVMIRKTAT GHSAYVAKKD LEELIVEMEN PALWGGKVTL ANGWQLELPA MAADTPLPIT VEARKL

Formula weight

7247.474 Da

Source organism

Escherichia coli

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.5 %, Completeness: 92.0 %, Completeness (bb): 94.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.0 % (706 of 767)	94.0 % (373 of 397)	89.4 % (271 of 303)	92.5 % (62 of 67)
Backbone	94.8 % (368 of 388)	96.2 % (127 of 132)	94.3 % (183 of 194)	93.5 % (58 of 62)
Sidechain	90.5 % (399 of 441)	92.8 % (246 of 265)	87.1 % (149 of 171)	80.0 % (4 of 5)
Aromatic	30.6 % (11 of 36)	50.0 % (9 of 18)	0.0 % (0 of 16)	100.0 % (2 of 2)
Methyl	97.8 % (90 of 92)	97.8 % (45 of 46)	97.8 % (45 of 46)

1. RP4601

MKVMIRKTAT GHSAYVAKKD LEELIVEMEN PALWGGKVTL ANGWQLELPA MAADTPLPIT VEARKL

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.0

#	Name	Isotope labeling	Type	Concentration
1	RP4601	[U-100% 13C; U-100% 15N]		0.7 ~ 1.2 mM
2	NaN3			0.01 %
3	Zn			10 uM
4	DTT			10 mM
5	H2O			90 %
6	D2O			10 %
7	Benzamidine			1 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5.0

#	Name	Isotope labeling	Type	Concentration
8	RP4601	[U-100% 13C; U-100% 15N]		0.6 ~ 1.1 mM
9	D2O			100 %
10	NaN3			0.01 %
11	Zn			10 uM
12	DTT			10 mM
13	Benzamidine			1 mM

LACS Plot; CA

Referencing offset: 0.3 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 0.3 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.09 ppm, Outliers: 2 Detail

LACS Plot; CO

Referencing offset: 0.89 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2JN4, Strand ID: A Detail

Release date

2007-02-08

Citation

Assignment of a hypothetical protein RP4601 from Rhodopseudomonas palustris
Lemak, A.

Related entities 1. RP4601 assembly, : 1 : 7 entities Detail

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.0

#	Name	Isotope labeling	Type	Concentration
1	RP4601	[U-100% 13C; U-100% 15N]		0.7 ~ 1.2 mM
2	NaN3			0.01 %
3	Zn			10 uM
4	DTT			10 mM
5	H2O			90 %
6	D2O			10 %
7	Benzamidine			1 mM

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.0

#	Name	Isotope labeling	Type	Concentration
1	RP4601	[U-100% 13C; U-100% 15N]		0.7 ~ 1.2 mM
2	NaN3			0.01 %
3	Zn			10 uM
4	DTT			10 mM
5	H2O			90 %
6	D2O			10 %
7	Benzamidine			1 mM

3 3D HNCA

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.0

#	Name	Isotope labeling	Type	Concentration
1	RP4601	[U-100% 13C; U-100% 15N]		0.7 ~ 1.2 mM
2	NaN3			0.01 %
3	Zn			10 uM
4	DTT			10 mM
5	H2O			90 %
6	D2O			10 %
7	Benzamidine			1 mM

4 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 5.0

#	Name	Isotope labeling	Type	Concentration
1	RP4601	[U-100% 13C; U-100% 15N]		0.7 ~ 1.2 mM
2	NaN3			0.01 %
3	Zn			10 uM
4	DTT			10 mM
5	H2O			90 %
6	D2O			10 %
7	Benzamidine			1 mM

5 3D H(CCO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.0

#	Name	Isotope labeling	Type	Concentration
1	RP4601	[U-100% 13C; U-100% 15N]		0.7 ~ 1.2 mM
2	NaN3			0.01 %
3	Zn			10 uM
4	DTT			10 mM
5	H2O			90 %
6	D2O			10 %
7	Benzamidine			1 mM

6 HBHACBCAcoNH 4D projection Reconstruction

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.0

#	Name	Isotope labeling	Type	Concentration
1	RP4601	[U-100% 13C; U-100% 15N]		0.7 ~ 1.2 mM
2	NaN3			0.01 %
3	Zn			10 uM
4	DTT			10 mM
5	H2O			90 %
6	D2O			10 %
7	Benzamidine			1 mM

7 HCCCcoNH Tocsy 4D Projection Reconstruction

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.0

#	Name	Isotope labeling	Type	Concentration
1	RP4601	[U-100% 13C; U-100% 15N]		0.7 ~ 1.2 mM
2	NaN3			0.01 %
3	Zn			10 uM
4	DTT			10 mM
5	H2O			90 %
6	D2O			10 %
7	Benzamidine			1 mM

8 3D 1H-15N NOESY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.0

#	Name	Isotope labeling	Type	Concentration
1	RP4601	[U-100% 13C; U-100% 15N]		0.7 ~ 1.2 mM
2	NaN3			0.01 %
3	Zn			10 uM
4	DTT			10 mM
5	H2O			90 %
6	D2O			10 %
7	Benzamidine			1 mM

9 3D 1H-13C NOESY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.0

#	Name	Isotope labeling	Type	Concentration
1	RP4601	[U-100% 13C; U-100% 15N]		0.7 ~ 1.2 mM
2	NaN3			0.01 %
3	Zn			10 uM
4	DTT			10 mM
5	H2O			90 %
6	D2O			10 %
7	Benzamidine			1 mM

10 3D HN(COCA)CB

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.0

#	Name	Isotope labeling	Type	Concentration
1	RP4601	[U-100% 13C; U-100% 15N]		0.7 ~ 1.2 mM
2	NaN3			0.01 %
3	Zn			10 uM
4	DTT			10 mM
5	H2O			90 %
6	D2O			10 %
7	Benzamidine			1 mM

11 3D HCCH-TOCSY (H-Tocsy)

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5.0

#	Name	Isotope labeling	Type	Concentration
8	RP4601	[U-100% 13C; U-100% 15N]		0.6 ~ 1.1 mM
9	D2O			100 %
10	NaN3			0.01 %
11	Zn			10 uM
12	DTT			10 mM
13	Benzamidine			1 mM

12 HCCH-TOCSY (C-Tocsy)

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5.0

#	Name	Isotope labeling	Type	Concentration
8	RP4601	[U-100% 13C; U-100% 15N]		0.6 ~ 1.1 mM
9	D2O			100 %
10	NaN3			0.01 %
11	Zn			10 uM
12	DTT			10 mM
13	Benzamidine			1 mM

13 3D 1H-13C NOESY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5.0

#	Name	Isotope labeling	Type	Concentration
8	RP4601	[U-100% 13C; U-100% 15N]		0.6 ~ 1.1 mM
9	D2O			100 %
10	NaN3			0.01 %
11	Zn			10 uM
12	DTT			10 mM
13	Benzamidine			1 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15085_2jn4.nef
Input source #2: Coordindates	2jn4.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------
MGSSHHHHHHSSGRENLYFQGMKVMIRKTATGHSAYVAKKDLEELIVEMENPALWGGKVTLANGWQLELPAMAADTPLPITVEARKL
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGSSHHHHHHSSGRENLYFQGMKVMIRKTATGHSAYVAKKDLEELIVEMENPALWGGKVTLANGWQLELPAMAADTPLPITVEARKL
--------10--------20--------30--------40--------50--------60--------70--------80-------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	87	0	0	100.0

Content subtype: combined_15085_2jn4.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	699		74.7 (chain: A, length: 87)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	1766 (1)	noe	74.7 (chain: A, length: 87)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	64 (64)	.	58.6 (chain: A, length: 87)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 87, Sequence coverage: 74.7%
- Total number of assignments
  - ¹H chemical shifts: 370
  - ¹³C chemical shifts: 267
  - ¹⁵N chemical shifts: 62
- 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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 87, Sequence coverage: 74.7%
- Total number of restraints: 1764
- Weight of restraints: 1.0 (1764)
- Potential type of restraints: square-well-parabolic (1764)
- 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

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 87, Sequence coverage: 58.6%
- Total number of restraints: 64
- Total number of restraints per polymer type: 64
- Weight of restraints: 1.0 (64)
- Potential type of restraints: square-well-parabolic (64)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A