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BMRB: 27435

6E3C

NMR assignments of Decorator, a phage-cementing 15 KDa monomer

Authors

Newcomer, R.L., Belato, H., Teschke, C.M., Alexandrescu, A.T.

Assembly

Decorator monomer

Entity

1. Decorator monomer (polymer, Thiol state: not present), 137 monomers, 14365.60 Da Detail

GSHMANPNFT PSWPLYKDAD GVYVSALPIK AIKYANDGSA NAEFDGPYAD QYMSAQTVAV FKPEVGGYLF RSQYGELLYM SKTAFEANYT SASGSVANAE TADKLSTART ITLTGAVTGS ASFDGSANVT IETTSGS

Formula weight

14365.6 Da

Source organism

Enterobacteria phage L

Exptl. method

solution NMR

Refine. method

simulated annealingsimulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 82.5 %, Completeness (bb): 97.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	82.5 % (1211 of 1467)	82.3 % (611 of 742)	78.6 % (458 of 583)	100.0 % (142 of 142)
Backbone	97.5 % (790 of 810)	95.7 % (268 of 280)	98.0 % (391 of 399)	100.0 % (131 of 131)
Sidechain	69.4 % (543 of 782)	74.2 % (343 of 462)	61.2 % (189 of 309)	100.0 % (11 of 11)
Aromatic	28.4 % (42 of 148)	55.4 % (41 of 74)	0.0 % (0 of 73)	100.0 % (1 of 1)
Methyl	83.1 % (118 of 142)	90.1 % (64 of 71)	76.1 % (54 of 71)

1. Decorator

GSHMANPNFT PSWPLYKDAD GVYVSALPIK AIKYANDGSA NAEFDGPYAD QYMSAQTVAV FKPEVGGYLF RSQYGELLYM SKTAFEANYT SASGSVANAE TADKLSTART ITLTGAVTGS ASFDGSANVT IETTSGS

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 4, Details The pH of the sample was lowered to 2 for a brief period, before being raised to pH 4.02.

#	Name	Isotope labeling	Concentration
1	sodium acetate	natural abundance	20 mM
2	sodium chloride	natural abundance	50 mM
3	EDTA	natural abundance	1 mM
4	Decorator	[U-100% 13C; U-100% 15N; U-80% 2H]	0.08 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 4, Details Two separate samples had their pH lowered to 2 for a period of 5 minutes before being raised to 4. The two samples were pooled together and lyophilized.

#	Name	Isotope labeling	Concentration
5	sodium acetate	natural abundance	40 mM
6	sodium chloride	natural abundance	100 mM
7	EDTA	natural abundance	2 mM
8	Decorator	[U-10% 13C; U-100% 15N]	1 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 4, Details pH was raised to 4.05 after being unfolded at pH 1.97 for 2 minutes.

#	Name	Isotope labeling	Concentration
9	sodium acetate	natural abundance	20 mM
10	sodium chloride	natural abundance	50 mM
11	EDTA	natural abundance	1 mM
12	Decorator	[U-100% 15N]	0.15 mM

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 4, Details The sample was unfolded to pH 2 for a period of time before being refolded at pH 4.

#	Name	Isotope labeling	Concentration
13	Decorator	[U-100% 13C; U-100% 15N; U-50% 2H]	0.2 mM
14	sodium acetate	natural abundance	20 mM
15	sodium chloride	natural abundance	50 mM
16	EDTA	natural abundance	1 mM

LACS Plot; CA

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

Referencing offset: 0.45 ppm, Outliers: 2 Detail

LACS Plot; CB

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

Referencing offset: 0.45 ppm, Outliers: 2 Detail

LACS Plot; HA

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

Referencing offset: -0.02 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: 0.2 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 6E3C, Strand ID: C Detail

Release date

2018-03-27

Citation

NMR assignments for monomeric phage L decoration protein
Newcomer, R.L., Belato, H., Teschke, C.M., Alexandrescu, A.T.
Biomol. NMR Assign. (2018), 12, 339-343, PubMed 30109462 , DOI 10.1007/s12104-018-9836-1 , Abstract

Related entities 1. Decorator monomer, : 1 entities Detail

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 4, Details The pH of the sample was lowered to 2 for a brief period, before being raised to pH 4.02.

#	Name	Isotope labeling	Concentration
1	sodium acetate	natural abundance	20 mM
2	sodium chloride	natural abundance	50 mM
3	EDTA	natural abundance	1 mM
4	Decorator	[U-100% 13C; U-100% 15N; U-80% 2H]	0.08 mM

2 3D HNCA

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	sodium acetate	natural abundance	20 mM
2	sodium chloride	natural abundance	50 mM
3	EDTA	natural abundance	1 mM
4	Decorator	[U-100% 13C; U-100% 15N; U-80% 2H]	0.08 mM

3 3D HN(CO)CA

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	sodium acetate	natural abundance	20 mM
2	sodium chloride	natural abundance	50 mM
3	EDTA	natural abundance	1 mM
4	Decorator	[U-100% 13C; U-100% 15N; U-80% 2H]	0.08 mM

4 3D HNCACB

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	sodium acetate	natural abundance	20 mM
2	sodium chloride	natural abundance	50 mM
3	EDTA	natural abundance	1 mM
4	Decorator	[U-100% 13C; U-100% 15N; U-80% 2H]	0.08 mM

5 3D HNCO

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	sodium acetate	natural abundance	20 mM
2	sodium chloride	natural abundance	50 mM
3	EDTA	natural abundance	1 mM
4	Decorator	[U-100% 13C; U-100% 15N; U-80% 2H]	0.08 mM

6 3D HN(CA)CO

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	sodium acetate	natural abundance	20 mM
2	sodium chloride	natural abundance	50 mM
3	EDTA	natural abundance	1 mM
4	Decorator	[U-100% 13C; U-100% 15N; U-80% 2H]	0.08 mM

7 3D HCCH-TOCSY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 4, Details Two separate samples had their pH lowered to 2 for a period of 5 minutes before being raised to 4. The two samples were pooled together and lyophilized.

#	Name	Isotope labeling	Concentration
5	sodium acetate	natural abundance	40 mM
6	sodium chloride	natural abundance	100 mM
7	EDTA	natural abundance	2 mM
8	Decorator	[U-10% 13C; U-100% 15N]	1 mM

8 3D CCH-TOCSY

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
5	sodium acetate	natural abundance	40 mM
6	sodium chloride	natural abundance	100 mM
7	EDTA	natural abundance	2 mM
8	Decorator	[U-10% 13C; U-100% 15N]	1 mM

9 3D 1H-15N TOCSY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 4, Details pH was raised to 4.05 after being unfolded at pH 1.97 for 2 minutes.

#	Name	Isotope labeling	Concentration
9	sodium acetate	natural abundance	20 mM
10	sodium chloride	natural abundance	50 mM
11	EDTA	natural abundance	1 mM
12	Decorator	[U-100% 15N]	0.15 mM

10 3D 1H-15N NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 4, Details pH was raised to 4.05 after being unfolded at pH 1.97 for 2 minutes.

#	Name	Isotope labeling	Concentration
9	sodium acetate	natural abundance	20 mM
10	sodium chloride	natural abundance	50 mM
11	EDTA	natural abundance	1 mM
12	Decorator	[U-100% 15N]	0.15 mM

11 3D 1H-15N NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 273 K, pH 4, Details The sample was unfolded to pH 2 for a period of time before being refolded at pH 4.

#	Name	Isotope labeling	Concentration
13	Decorator	[U-100% 13C; U-100% 15N; U-50% 2H]	0.2 mM
14	sodium acetate	natural abundance	20 mM
15	sodium chloride	natural abundance	50 mM
16	EDTA	natural abundance	1 mM

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_27435_6e3c.nef
Input source #2: Coordindates	6e3c.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): C vs Auth_asym_ID (model): C

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
C	C	137	0	0	100.0

Content subtype: combined_27435_6e3c.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1212		100.0 (chain: C, length: 137)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	185 (1)	noe	59.9 (chain: C, length: 137)
2	Distance restraints	CNS/XPLOR_distance_constraints_5	Warning	787 (1)	noe	95.6 (chain: C, length: 137)
3	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	67 (1)	hbond	36.5 (chain: C, length: 137)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	174 (174)	.	73.0 (chain: C, length: 137)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: C, Chain length: 137, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 611
  - ¹³C chemical shifts: 460
  - ¹⁵N chemical shifts: 141
- Completeness of assignments
  - Entity_assemble_ID: C
- 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: C

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	742	611	82.3
¹³C chemical shifts	583	460	78.9
¹⁵N chemical shifts	144	141	97.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	280	275	98.2
¹³C chemical shifts	274	274	100.0
¹⁵N chemical shifts	131	130	99.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	462	336	72.7
¹³C chemical shifts	309	186	60.2
¹⁵N chemical shifts	13	11	84.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	74	64	86.5
¹³C chemical shifts	74	53	71.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	74	39	52.7
¹³C chemical shifts	73	0	0.0
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: C, Chain length: 137, Sequence coverage: 59.9%
- Total number of restraints: 184
- Weight of restraints: 1.0 (184)
- Potential type of restraints: square-well-parabolic (184)
- Range of distance target values: 2.42, 6.13 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: C
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_5
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: C, Chain length: 137, Sequence coverage: 95.6%
  - Total number of restraints: 787
  - Weight of restraints: 1.0 (787)
  - Potential type of restraints: square-well-parabolic (787)
  - Range of distance target values: 2.24, 6.64 (Å)
  - Histogram of distance target values
  - Histogram of discrepancy in distance target values
  - Distance restraints per residue
    - Chain_ID: C
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_4
    - Status: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: C, Chain length: 137, Sequence coverage: 36.5%
    - Total number of restraints: 67
    - Weight of restraints: 1.0 (67)
    - Potential type of restraints: square-well-parabolic (67)
    - Range of distance target values: 2.21, 3.32 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: C
    - 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: C, Chain length: 137, Sequence coverage: 73.0%
- Total number of restraints: 174
- Total number of restraints per polymer type: 174
- Weight of restraints: 1.0 (174)
- Potential type of restraints: square-well-parabolic (174)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: C

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Found 1 Document (0.576 seconds)

BMRB: 27435

Sample #1

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Sample #3

Sample #4

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Decorator monomer, : 1 entities Detail

Experiments performed 11 experiments Detail

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NMR combined restraints 6 contents Detail