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BMRB: 34139

5O1Q

LysF1 sh3b domain structure

Authors

Benesik, M., Novacek, J., Janda, L., Dopitova, R., Pernisova, M., Melkova, K., Tisakova, L., Doskar, J., Zidek, L., Hejatko, J., Pantucek, R.

Assembly

sh3b domain

Entity

1. sh3b domain (polymer), 106 monomers, 11521.91 Da Detail

ETPATRPVTG SWKKNQYGTW YKPENATFVN GNQPIVTRIG SPFLNAPVGG NLPAGATIVY DEVCIQAGHI WIGYNAYNGN RVYCPVRTCQ GVPPNQIPGV AWGVFK

Formula weight

11521.91 Da

Source organism

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.1 %, Completeness: 94.2 %, Completeness (bb): 97.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	94.2 % (1145 of 1216)	93.6 % (589 of 629)	93.9 % (444 of 473)	98.2 % (112 of 114)
Backbone	97.9 % (601 of 614)	97.7 % (209 of 214)	98.0 % (299 of 305)	97.9 % (93 of 95)
Sidechain	91.5 % (636 of 695)	91.6 % (380 of 415)	90.8 % (237 of 261)	100.0 % (19 of 19)
Aromatic	70.8 % (92 of 130)	70.8 % (46 of 65)	68.9 % (42 of 61)	100.0 % (4 of 4)
Methyl	100.0 % (112 of 112)	100.0 % (56 of 56)	100.0 % (56 of 56)

1. entity 1

ETPATRPVTG SWKKNQYGTW YKPENATFVN GNQPIVTRIG SPFLNAPVGG NLPAGATIVY DEVCIQAGHI WIGYNAYNGN RVYCPVRTCQ GVPPNQIPGV AWGVFK

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20 mM Na-phosphate, 0.25 mM [U-99% 13C; U-99% 15N] sh3b domain, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Na-phosphate	natural abundance		20 mM
2	sh3b domain	[U-99% 13C; U-99% 15N]		0.25 mM

LACS Plot; CA

Referencing offset: 0.1 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: 0.1 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: -0.12 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.48 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 5O1Q, Strand ID: A Detail

Release date

2017-09-10

Citation

Role of SH3b binding domain in a natural deletion mutant of Kayvirus endolysin LysF1 with a broad range of lytic activity
Benesik, M., Novacek, J., Janda, L., Dopitova, R., Pernisova, M., Melkova, K., Tisakova, L., Doskar, J., Zidek, L., Hejatko, J., Pantucek, R.
Virus Genes (2017), 54, 130-139, PubMed 28852930 , DOI 10.1007/s11262-017-1507-2 , Abstract

Related entities 1. sh3b domain, : 1 : 1 : 11 entities Detail

Experiments performed 11 experiments Detail

1 3D HNCO

Instrument

Bruker AvanceII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20 mM Na-phosphate, 0.25 mM [U-99% 13C; U-99% 15N] sh3b domain, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Na-phosphate	natural abundance		20 mM
2	sh3b domain	[U-99% 13C; U-99% 15N]		0.25 mM

2 3D HN(CA)CO

Instrument

Bruker AvanceII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20 mM Na-phosphate, 0.25 mM [U-99% 13C; U-99% 15N] sh3b domain, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Na-phosphate	natural abundance		20 mM
2	sh3b domain	[U-99% 13C; U-99% 15N]		0.25 mM

3 3D HNCACB

Instrument

Bruker AvanceII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20 mM Na-phosphate, 0.25 mM [U-99% 13C; U-99% 15N] sh3b domain, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Na-phosphate	natural abundance		20 mM
2	sh3b domain	[U-99% 13C; U-99% 15N]		0.25 mM

4 3D CBCA(CO)NH

Instrument

Bruker AvanceII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20 mM Na-phosphate, 0.25 mM [U-99% 13C; U-99% 15N] sh3b domain, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Na-phosphate	natural abundance		20 mM
2	sh3b domain	[U-99% 13C; U-99% 15N]		0.25 mM

5 3D HNCA

Instrument

Bruker AvanceII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20 mM Na-phosphate, 0.25 mM [U-99% 13C; U-99% 15N] sh3b domain, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Na-phosphate	natural abundance		20 mM
2	sh3b domain	[U-99% 13C; U-99% 15N]		0.25 mM

6 3D HN(CO)CA

Instrument

Bruker AvanceII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20 mM Na-phosphate, 0.25 mM [U-99% 13C; U-99% 15N] sh3b domain, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Na-phosphate	natural abundance		20 mM
2	sh3b domain	[U-99% 13C; U-99% 15N]		0.25 mM

7 3D HCCH-TOCSY

Instrument

Bruker AvanceII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20 mM Na-phosphate, 0.25 mM [U-99% 13C; U-99% 15N] sh3b domain, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Na-phosphate	natural abundance		20 mM
2	sh3b domain	[U-99% 13C; U-99% 15N]		0.25 mM

8 3D HNH NOESY

Instrument

Bruker AvanceII - 950 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20 mM Na-phosphate, 0.25 mM [U-99% 13C; U-99% 15N] sh3b domain, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Na-phosphate	natural abundance		20 mM
2	sh3b domain	[U-99% 13C; U-99% 15N]		0.25 mM

9 3D HCH NOESY

Instrument

Bruker AvanceII - 950 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20 mM Na-phosphate, 0.25 mM [U-99% 13C; U-99% 15N] sh3b domain, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Na-phosphate	natural abundance		20 mM
2	sh3b domain	[U-99% 13C; U-99% 15N]		0.25 mM

10 3D HCH NOESY

Instrument

Bruker AvanceII - 950 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20 mM Na-phosphate, 0.25 mM [U-99% 13C; U-99% 15N] sh3b domain, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Na-phosphate	natural abundance		20 mM
2	sh3b domain	[U-99% 13C; U-99% 15N]		0.25 mM

11 1D H

Instrument

Bruker AvanceII - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20 mM Na-phosphate, 0.25 mM [U-99% 13C; U-99% 15N] sh3b domain, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	Na-phosphate	natural abundance		20 mM
2	sh3b domain	[U-99% 13C; U-99% 15N]		0.25 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_34139_5o1q.nef
Input source #2: Coordindates	5o1q.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
ETPATRPVTGSWKKNQYGTWYKPENATFVNGNQPIVTRIGSPFLNAPVGGNLPAGATIVYDEVCIQAGHIWIGYNAYNGNRVYCPVRTCQGVPPNQIPGV
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ETPATRPVTGSWKKNQYGTWYKPENATFVNGNQPIVTRIGSPFLNAPVGGNLPAGATIVYDEVCIQAGHIWIGYNAYNGNRVYCPVRTCQGVPPNQIPGV

------
AWGVFK
||||||
AWGVFK

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	106	0	0	100.0

Content subtype: combined_34139_5o1q.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1133		99.1 (chain: A, length: 106)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	3235 (1)	noe	98.1 (chain: A, length: 106)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	150 (150)	.	90.6 (chain: A, length: 106)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 106, Sequence coverage: 99.1%
- Total number of assignments
  - ¹H chemical shifts: 583
  - ¹³C chemical shifts: 439
  - ¹⁵N chemical shifts: 111
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- 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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 106, Sequence coverage: 98.1%
- Total number of restraints: 3235
- Weight of restraints: 1.0 (3235)
- Potential type of restraints: square-well-parabolic (3235)
- Range of distance target values: 1.15, 3.12 (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_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 106, Sequence coverage: 90.6%
- Total number of restraints: 150
- Total number of restraints per polymer type: 150
- Weight of restraints: 1.0 (150)
- Potential type of restraints: square-well-parabolic (150)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords endolysin, hydrolase, sh3b