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Found 1 Document (0.64 seconds)

BMRB: 30185

5TGW

NMR structure of apo-PS1

Authors

Polizzi, N.F., Wu, Y.

Assembly

PS1

Entity

1. PS1 (polymer, Thiol state: not present), 109 monomers, 12947.12 Da Detail

SEFEKLRQTG DELVQAFQRL REIFDKGDDD SLEQVLEEIE ELIQKHRQLF DNRQEAADTE AAKQGDQWVQ LFQRFREAID KGDKDSLEQL LEELEQALQK IRELAEKKN

Formula weight

12947.12 Da

Source organism

Escherichia coli

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 97.2 %, Completeness: 84.5 %, Completeness (bb): 78.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	84.5 % (1131 of 1338)	90.7 % (646 of 712)	74.4 % (372 of 500)	89.7 % (113 of 126)
Backbone	78.1 % (511 of 654)	90.5 % (201 of 222)	66.3 % (214 of 323)	88.1 % (96 of 109)
Sidechain	91.4 % (721 of 789)	90.8 % (445 of 490)	91.8 % (259 of 282)	100.0 % (17 of 17)
Aromatic	69.7 % (53 of 76)	78.9 % (30 of 38)	59.5 % (22 of 37)	100.0 % (1 of 1)
Methyl	97.2 % (105 of 108)	94.4 % (51 of 54)	100.0 % (54 of 54)

1. PS1

SEFEKLRQTG DELVQAFQRL REIFDKGDDD SLEQVLEEIE ELIQKHRQLF DNRQEAADTE AAKQGDQWVQ LFQRFREAID KGDKDSLEQL LEELEQALQK IRELAEKKN

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 780 uM [U-100% 13C; U-100% 15N] apo-PS1, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	apo-PS1	[U-100% 13C; U-100% 15N]	780 uM
2	NaPi	natural abundance	100 mM
3	NaCl	natural abundance	50 mM
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 780 uM U-100% 15N; 10% 13C] apo-PS1, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
6	apo-PS1	U-100% 15N; 10% 13C]	780 uM
7	NaPi	natural abundance	100 mM
8	NaCl	natural abundance	50 mM
9	H2O	natural abundance	95 %
10	D2O	natural abundance	5 %

LACS Plot; CA

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

Referencing offset: 0.07 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: 0.07 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: 0.08 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 5TGW, Strand ID: A Detail

Release date

2016-11-13

Citation

De novo design of a hyperstable non-natural protein-ligand complex with sub-Å accuracy
Polizzi, N.F., Wu, Y., Lemmin, T., Maxwell, A.M., Zhang, S.Q., Rawson, J., Beratan, D.N., Therien, M.J., DeGrado, W.F.
Nat. Chem. (2017), 9, 1157-1164, PubMed 29168496 , DOI 10.1038/nchem.2846 , Abstract

Related entities 1. PS1, : 1 : 1 : 1 : 35 entities Detail

Experiments performed 9 experiments Detail

1 3D HNCACB

Instrument

Bruker AvanceII - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 780 uM [U-100% 13C; U-100% 15N] apo-PS1, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	apo-PS1	[U-100% 13C; U-100% 15N]	780 uM
2	NaPi	natural abundance	100 mM
3	NaCl	natural abundance	50 mM
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

2 3D CBCA(CO)NH

Instrument

Bruker AvanceII - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 780 uM [U-100% 13C; U-100% 15N] apo-PS1, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	apo-PS1	[U-100% 13C; U-100% 15N]	780 uM
2	NaPi	natural abundance	100 mM
3	NaCl	natural abundance	50 mM
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

3 3D HNCO

Instrument

Bruker AvanceII - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 780 uM [U-100% 13C; U-100% 15N] apo-PS1, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	apo-PS1	[U-100% 13C; U-100% 15N]	780 uM
2	NaPi	natural abundance	100 mM
3	NaCl	natural abundance	50 mM
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

4 3D CO(CA)NH

Instrument

Bruker AvanceII - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 780 uM [U-100% 13C; U-100% 15N] apo-PS1, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	apo-PS1	[U-100% 13C; U-100% 15N]	780 uM
2	NaPi	natural abundance	100 mM
3	NaCl	natural abundance	50 mM
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

5 3D CCH-TOCSY

Instrument

Bruker AvanceII - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 780 uM [U-100% 13C; U-100% 15N] apo-PS1, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	apo-PS1	[U-100% 13C; U-100% 15N]	780 uM
2	NaPi	natural abundance	100 mM
3	NaCl	natural abundance	50 mM
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

6 3D 15N-13Caliphatic-13Caromatic-resolved [1H-1H]-NOESY

Instrument

Bruker AvanceII - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 780 uM [U-100% 13C; U-100% 15N] apo-PS1, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	apo-PS1	[U-100% 13C; U-100% 15N]	780 uM
2	NaPi	natural abundance	100 mM
3	NaCl	natural abundance	50 mM
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

7 2D 1H-13C HSQC aliphatic

Instrument

Bruker AvanceII - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 780 uM U-100% 15N; 10% 13C] apo-PS1, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
6	apo-PS1	U-100% 15N; 10% 13C]	780 uM
7	NaPi	natural abundance	100 mM
8	NaCl	natural abundance	50 mM
9	H2O	natural abundance	95 %
10	D2O	natural abundance	5 %

8 3D simultaneous NOESY

Instrument

Bruker AvanceII - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 780 uM [U-100% 13C; U-100% 15N] apo-PS1, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	apo-PS1	[U-100% 13C; U-100% 15N]	780 uM
2	NaPi	natural abundance	100 mM
3	NaCl	natural abundance	50 mM
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

9 2D 1H-15N HSQC

Instrument

Bruker AvanceII - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 780 uM [U-100% 13C; U-100% 15N] apo-PS1, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	apo-PS1	[U-100% 13C; U-100% 15N]	780 uM
2	NaPi	natural abundance	100 mM
3	NaCl	natural abundance	50 mM
4	H2O	natural abundance	95 %
5	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_30185_5tgw.nef
Input source #2: Coordindates	5tgw.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
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||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SEFEKLRQTGDELVQAFQRLREIFDKGDDDSLEQVLEEIEELIQKHRQLFDNRQEAADTEAAKQGDQWVQLFQRFREAIDKGDKDSLEQLLEELEQALQK

---------
IRELAEKKN
|||||||||
IRELAEKKN

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	109	0	0	100.0

Content subtype: combined_30185_5tgw.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1143		96.3 (chain: A, length: 109)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	934 (1)	noe	77.1 (chain: A, length: 109)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	210 (210)	.	94.5 (chain: A, length: 109)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 109, Sequence coverage: 96.3%
- Total number of assignments
  - ¹H chemical shifts: 674
  - ¹³C chemical shifts: 361
  - ¹⁵N chemical shifts: 108
- Completeness of assignments
  - Entity_assemble_ID: A
- Tautomeric state of HIS
- 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)
46	HIS	HD1	7.258

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	712	673	94.5
¹³C chemical shifts	500	361	72.2
¹⁵N chemical shifts	134	108	80.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	222	208	93.7
¹³C chemical shifts	218	102	46.8
¹⁵N chemical shifts	109	90	82.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	490	465	94.9
¹³C chemical shifts	282	259	91.8
¹⁵N chemical shifts	25	18	72.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	54	54	100.0
¹³C chemical shifts	54	54	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	38	33	86.8
¹³C chemical shifts	37	22	59.5
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 109, Sequence coverage: 77.1%
- Total number of restraints: 934
- Weight of restraints: 1.0 (934)
- Potential type of restraints: square-well-parabolic (934)
- Range of distance target values: 2.36, 4.81 (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_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 109, Sequence coverage: 94.5%
- Total number of restraints: 210
- Total number of restraints per polymer type: 210
- Weight of restraints: 1.0 (210)
- Potential type of restraints: square-well-parabolic (210)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords 4-helix bundle, UNKNOWN FUNCTION, coiled-coil

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Found 1 Document (0.64 seconds)

BMRB: 30185

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. PS1, : 1 : 1 : 1 : 35 entities Detail

Experiments performed 9 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

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Sample

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Sample

NMR combined restraints 4 contents Detail