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BMRB: 25994

2NBS

Backbone 1H, 13C, and 15N Chemical Shift Assignments for designed protein E_1r26

Authors

Assembly

designed protein E 1r26

Entity

1. designed protein E 1r26 (polymer, Thiol state: not present), 122 monomers, 13964.62 Da Detail

MARPSNVKPS PHVIKSLEEL REATASNRIS VIVFTHPDSK RSKEIKEKLK KLAEEFPDVD IYLVDTSTNP EAREWYNITS VPTFVIEKGG EPLGEVKGPD IDKLRETLDE LLARLEHHHH HH

Formula weight

13964.62 Da

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.7 %, Completeness: 71.2 %, Completeness (bb): 80.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	71.2 % (1029 of 1446)	75.2 % (570 of 758)	61.9 % (353 of 570)	89.8 % (106 of 118)
Backbone	80.4 % (574 of 714)	89.5 % (214 of 239)	70.4 % (255 of 362)	92.9 % (105 of 113)
Sidechain	66.1 % (562 of 850)	68.0 % (353 of 519)	64.1 % (209 of 326)	0.0 % (0 of 5)
Aromatic	6.7 % (6 of 90)	13.3 % (6 of 45)	0.0 % (0 of 44)	0.0 % (0 of 1)
Methyl	50.0 % (69 of 138)	53.6 % (37 of 69)	46.4 % (32 of 69)

1. E 1r26

MARPSNVKPS PHVIKSLEEL REATASNRIS VIVFTHPDSK RSKEIKEKLK KLAEEFPDVD IYLVDTSTNP EAREWYNITS VPTFVIEKGG EPLGEVKGPD IDKLRETLDE LLARLEHHHH HH

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]	protein	0.0 ~ 0.0 mM
2	sodium phosphate	natural abundance	buffer	0.02 mM
3	EDTA	natural abundance		0.01 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

LACS Plot; CA

Referencing offset: -0.06 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.06 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.05 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2016-10-12

Citation

Proteins of well-defined structures can be designed without backbone readjustment by a statistical model
Zhou, X., Xiong, P., Wang, M., Ma, R., Zhang, J., Chen, Q., Liu, H.
J. Struct. Biol. (2016), 196, 350-357, PubMed 27522946 , DOI 10.1016/j.jsb.2016.08.002 , Abstract

Related entities 1. designed protein E 1r26, : 1 : 110 entities Detail

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]	protein	0.0 ~ 0.0 mM
2	sodium phosphate	natural abundance	buffer	0.02 mM
3	EDTA	natural abundance		0.01 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

2 3D CBCA(CO)NH

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]	protein	0.0 ~ 0.0 mM
2	sodium phosphate	natural abundance	buffer	0.02 mM
3	EDTA	natural abundance		0.01 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

3 3D C(CO)NH

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]	protein	0.0 ~ 0.0 mM
2	sodium phosphate	natural abundance	buffer	0.02 mM
3	EDTA	natural abundance		0.01 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

4 3D HNCACB

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]	protein	0.0 ~ 0.0 mM
2	sodium phosphate	natural abundance	buffer	0.02 mM
3	EDTA	natural abundance		0.01 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

5 3D CBCA(CO)NH

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]	protein	0.0 ~ 0.0 mM
2	sodium phosphate	natural abundance	buffer	0.02 mM
3	EDTA	natural abundance		0.01 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

6 3D HBHA(CO)NH

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]	protein	0.0 ~ 0.0 mM
2	sodium phosphate	natural abundance	buffer	0.02 mM
3	EDTA	natural abundance		0.01 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

7 3D HN(CO)CA

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]	protein	0.0 ~ 0.0 mM
2	sodium phosphate	natural abundance	buffer	0.02 mM
3	EDTA	natural abundance		0.01 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

8 3D H(CCO)NH

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]	protein	0.0 ~ 0.0 mM
2	sodium phosphate	natural abundance	buffer	0.02 mM
3	EDTA	natural abundance		0.01 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

9 3D 1H-13C NOESY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]	protein	0.0 ~ 0.0 mM
2	sodium phosphate	natural abundance	buffer	0.02 mM
3	EDTA	natural abundance		0.01 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

10 3D 1H-15N TOCSY

Instrument

Bruker DMX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]	protein	0.0 ~ 0.0 mM
2	sodium phosphate	natural abundance	buffer	0.02 mM
3	EDTA	natural abundance		0.01 mM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25994_2nbs.nef
Input source #2: Coordindates	2nbs.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
MARPSNVKPSPHVIKSLEELREATASNRISVIVFTHPDSKRSKEIKEKLKKLAEEFPDVDIYLVDTSTNPEAREWYNITSVPTFVIEKGGEPLGEVKGPD
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MARPSNVKPSPHVIKSLEELREATASNRISVIVFTHPDSKRSKEIKEKLKKLAEEFPDVDIYLVDTSTNPEAREWYNITSVPTFVIEKGGEPLGEVKGPD

-------110-------120--
IDKLRETLDELLARLEHHHHHH
||||||||||||||||||||||
IDKLRETLDELLARLEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	122	0	0	100.0

Content subtype: combined_25994_2nbs.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	962		96.7 (chain: A, length: 122)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1322 (1)	noe	86.9 (chain: A, length: 122)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	46 (1)	hbond	27.9 (chain: A, length: 122)
3	Distance restraints	DYANA/DIANA_distance_constraints_5	Warning	46 (1)	hbond	27.9 (chain: A, length: 122)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_4	OK	146 (146)	.	77.0 (chain: A, length: 122)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 122, Sequence coverage: 96.7%
- Total number of assignments
  - ¹H chemical shifts: 545
  - ¹³C chemical shifts: 311
  - ¹⁵N chemical shifts: 106
- 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_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 122, Sequence coverage: 86.9%
- Total number of restraints: 1314
- Weight of restraints: 1.0 (1314)
- Potential type of restraints: square-well-parabolic (1314)
- Range of distance target values: 2.0, 5.7 (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: DYANA/DIANA_distance_constraints_3
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 122, Sequence coverage: 27.9%
  - Total number of restraints: 46
  - Weight of restraints: 1.0 (46)
  - Potential type of restraints: upper-bound-parabolic (46)
  - Range of distance target values: 2.5, 3.5 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: DYANA/DIANA_distance_constraints_5
    - Status: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 122, Sequence coverage: 27.9%
    - Total number of restraints: 46
    - Weight of restraints: 1.0 (46)
    - Potential type of restraints: upper-bound-parabolic (46)
    - Range of distance target values: 1.5, 2.5 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 122, Sequence coverage: 77.0%
- Total number of restraints: 146
- Total number of restraints per polymer type: 146
- Weight of restraints: 1.0 (146)
- Potential type of restraints: square-well-parabolic (146)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords designed protein