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Found 1 Document (0.705 seconds)

BMRB: 17304

2L69

Solution NMR Structure of de novo designed rossmann 2x3 fold protein, Northeast Structural Genomics Consortium Target OR28

Authors

Liu, G., Koga, N., Koga, R., Xiao, R., Mao, L., Mao, B., Patel, D., ciccosanti, C., Hamilton, K., Acton, T.B., Baker, D., Montelione, G.T.

Assembly

OR28

Entity

1. OR28 (polymer, Thiol state: not present), 134 monomers, 15825.95 Da Detail

MNIVIVVFST DEETLRKFKD IIKKNGFKVR TVRSPQELKD SIEELVKKYN ATIVVVVVDD KEWAEKAIRF VKSLGAQVLI IIYDQDQNRL EEFSREVRRR GFEVRTVTSP DDFKKSLERL IREVGSLEHH HHHH

Formula weight

15825.95 Da

Exptl. method

solution NMR

Refine. method

distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 94.8 %, Completeness: 85.0 %, Completeness (bb): 79.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	85.0 % (1404 of 1651)	90.3 % (781 of 865)	76.1 % (491 of 645)	93.6 % (132 of 141)
Backbone	79.1 % (633 of 800)	91.9 % (248 of 270)	65.8 % (262 of 398)	93.2 % (123 of 132)
Sidechain	90.8 % (891 of 981)	89.6 % (533 of 595)	92.6 % (349 of 377)	100.0 % (9 of 9)
Aromatic	74.6 % (91 of 122)	70.5 % (43 of 61)	78.3 % (47 of 60)	100.0 % (1 of 1)
Methyl	98.8 % (166 of 168)	97.6 % (82 of 84)	100.0 % (84 of 84)

1. OR28

MNIVIVVFST DEETLRKFKD IIKKNGFKVR TVRSPQELKD SIEELVKKYN ATIVVVVVDD KEWAEKAIRF VKSLGAQVLI IIYDQDQNRL EEFSREVRRR GFEVRTVTSP DDFKKSLERL IREVGSLEHH HHHH

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 6.5, Details 0.62 mM [U-100% 13C; U-100% 15N] OR28, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	OR28	[U-100% 13C; U-100% 15N]	0.62 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 6.5, Details 0.47 mM [U-5% 13C; U-100% 15N] OR28, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
4	OR28	[U-5% 13C; U-100% 15N]	0.47 mM
5	H2O	natural abundance	95 %
6	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: 0.15 ppm, Outliers: 1 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: 0.15 ppm, Outliers: 1 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: -0.06 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2L69, Strand ID: A Detail

Release date

2010-11-16

Citation

Role of backbone strain in de novo design of complex α/β protein structures
Koga, N., Koga, R., Liu, G., Castellanos, J., Montelione, G.T., Baker, D.
Nat. Commun. (2021), 12, 3921-3921, PubMed 34168113 , DOI 10.1038/s41467-021-24050-7 , Abstract

Related entities 1. OR28, : 1 : 17 entities Detail

Experiments performed 7 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 6.5, Details 0.62 mM [U-100% 13C; U-100% 15N] OR28, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	OR28	[U-100% 13C; U-100% 15N]	0.62 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 6.5, Details 0.47 mM [U-5% 13C; U-100% 15N] OR28, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
4	OR28	[U-5% 13C; U-100% 15N]	0.47 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

3 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 6.5, Details 0.62 mM [U-100% 13C; U-100% 15N] OR28, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	OR28	[U-100% 13C; U-100% 15N]	0.62 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %

4 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 6.5, Details 0.62 mM [U-100% 13C; U-100% 15N] OR28, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	OR28	[U-100% 13C; U-100% 15N]	0.62 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %

5 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 6.5, Details 0.62 mM [U-100% 13C; U-100% 15N] OR28, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	OR28	[U-100% 13C; U-100% 15N]	0.62 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %

6 3D 1H-13C arom NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 6.5, Details 0.62 mM [U-100% 13C; U-100% 15N] OR28, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	OR28	[U-100% 13C; U-100% 15N]	0.62 mM
2	H2O	natural abundance	95 %
3	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 atm, Temperature 313 K, pH 6.5, Details 0.62 mM [U-100% 13C; U-100% 15N] OR28, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	OR28	[U-100% 13C; U-100% 15N]	0.62 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17304_2l69.nef
Input source #2: Coordindates	2l69.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
MNIVIVVFSTDEETLRKFKDIIKKNGFKVRTVRSPQELKDSIEELVKKYNATIVVVVVDDKEWAEKAIRFVKSLGAQVLIIIYDQDQNRLEEFSREVRRR
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MNIVIVVFSTDEETLRKFKDIIKKNGFKVRTVRSPQELKDSIEELVKKYNATIVVVVVDDKEWAEKAIRFVKSLGAQVLIIIYDQDQNRLEEFSREVRRR

-------110-------120-------130----
GFEVRTVTSPDDFKKSLERLIREVGSLEHHHHHH
||||||||||||||||||||||||||||||||||
GFEVRTVTSPDDFKKSLERLIREVGSLEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	134	0	0	100.0

Content subtype: combined_17304_2l69.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1420		94.8 (chain: A, length: 134)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	3526 (1)	noe	94.0 (chain: A, length: 134)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	200 (200)	.	88.1 (chain: A, length: 134)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 134, Sequence coverage: 94.8%
- Total number of assignments
  - ¹H chemical shifts: 807
  - ¹³C chemical shifts: 481
  - 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	865	807	93.3
¹³C chemical shifts	645	481	74.6
¹⁵N chemical shifts	153	132	86.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	270	254	94.1
¹³C chemical shifts	268	126	47.0
¹⁵N chemical shifts	132	123	93.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	595	553	92.9
¹³C chemical shifts	377	355	94.2
¹⁵N chemical shifts	21	9	42.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	85	84	98.8
¹³C chemical shifts	85	84	98.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	61	48	78.7
¹³C chemical shifts	60	47	78.3
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 134, Sequence coverage: 94.0%
- Total number of restraints: 3526
- Weight of restraints: 1.0 (3526)
- Potential type of restraints: square-well-parabolic (3526)
- Range of distance target values: 2.1, 4.2 (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: 134, Sequence coverage: 88.1%
- Total number of restraints: 200
- Total number of restraints per polymer type: 200
- Weight of restraints: 1.0 (200)
- Potential type of restraints: square-well-parabolic (200)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG), PSI-2, Protein NMR, Protein Structure Initiative, Structural Genomics, Target OR28

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Found 1 Document (0.705 seconds)

BMRB: 17304

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. OR28, : 1 : 17 entities Detail

Experiments performed 7 experiments Detail

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NMR combined restraints 4 contents Detail