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BMRB: 34325

6I2O

Solution NMR structure of PilE1 from Streptococcus sanguinis

Authors

Berry, J.L., Xu, Y.

Assembly

Type IV pilin PilE1

Entity

1. Type IV pilin PilE1 (polymer, Thiol state: not present), 113 monomers, 12069.94 Da Detail

HQDNARKSRI QSEHRELVSA IQSYIGAQDD PTNPSEITLA KLAPYMSKNA KNEDGIVNSL AKDKSGNSST SAPGSAHQID TTNHKLISTF TPSNGGQATV LTYDWSANGV NSN

Formula weight

12069.94 Da

Source organism

Streptococcus sanguinis

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 94.4 %, Completeness (bb): 99.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	94.4 % (1161 of 1230)	93.1 % (593 of 637)	98.5 % (460 of 467)	85.7 % (108 of 126)
Backbone	99.0 % (661 of 668)	98.7 % (225 of 228)	99.4 % (330 of 332)	98.1 % (106 of 108)
Sidechain	90.6 % (605 of 668)	90.0 % (368 of 409)	97.5 % (235 of 241)	11.1 % (2 of 18)
Aromatic	87.1 % (54 of 62)	90.3 % (28 of 31)	83.3 % (25 of 30)	100.0 % (1 of 1)
Methyl	100.0 % (108 of 108)	100.0 % (54 of 54)	100.0 % (54 of 54)

1. entity 1

HQDNARKSRI QSEHRELVSA IQSYIGAQDD PTNPSEITLA KLAPYMSKNA KNEDGIVNSL AKDKSGNSST SAPGSAHQID TTNHKLISTF TPSNGGQATV LTYDWSANGV NSN

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 750 nM [U-13C; U-15N] PilE1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	PilE1	[U-13C; U-15N]		750 nM
2	Sodium Phosphate	natural abundance		750 mM
3	NaCl	natural abundance		750 mM

LACS Plot; CA

Referencing offset: -0.19 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.19 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.02 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.16 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 6I2O, Strand ID: A Detail

Release date

2018-12-02

Citation

Global biochemical and structural analysis of the type IV pilus from the Gram-positive bacterium Streptococcus sanguinis
Berry, J.L., Gurung, I., Anonsen, J.H., Spielman, I., Harper, E., Hall, A., Goosens, V.J., Raynaud, C., Koomey, M., Biais, N., Matthews, S., Pelicic, V.
J. Biol. Chem. (2019), 294, 6796-6808, PubMed 30837269 , DOI 10.1074/jbc.RA118.006917 , Abstract

Related entities 1. Type IV pilin PilE1, : 1 : 1 entities Detail

Experiments performed 10 experiments Detail

1 3D HBHA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 750 nM [U-13C; U-15N] PilE1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	PilE1	[U-13C; U-15N]		750 nM
2	Sodium Phosphate	natural abundance		750 mM
3	NaCl	natural abundance		750 mM

2 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 750 nM [U-13C; U-15N] PilE1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	PilE1	[U-13C; U-15N]		750 nM
2	Sodium Phosphate	natural abundance		750 mM
3	NaCl	natural abundance		750 mM

3 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 750 nM [U-13C; U-15N] PilE1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	PilE1	[U-13C; U-15N]		750 nM
2	Sodium Phosphate	natural abundance		750 mM
3	NaCl	natural abundance		750 mM

4 3D HN(CO)CA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 750 nM [U-13C; U-15N] PilE1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	PilE1	[U-13C; U-15N]		750 nM
2	Sodium Phosphate	natural abundance		750 mM
3	NaCl	natural abundance		750 mM

5 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 750 nM [U-13C; U-15N] PilE1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	PilE1	[U-13C; U-15N]		750 nM
2	Sodium Phosphate	natural abundance		750 mM
3	NaCl	natural abundance		750 mM

6 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 750 nM [U-13C; U-15N] PilE1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	PilE1	[U-13C; U-15N]		750 nM
2	Sodium Phosphate	natural abundance		750 mM
3	NaCl	natural abundance		750 mM

7 3D H(CCO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 750 nM [U-13C; U-15N] PilE1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	PilE1	[U-13C; U-15N]		750 nM
2	Sodium Phosphate	natural abundance		750 mM
3	NaCl	natural abundance		750 mM

8 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 750 nM [U-13C; U-15N] PilE1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	PilE1	[U-13C; U-15N]		750 nM
2	Sodium Phosphate	natural abundance		750 mM
3	NaCl	natural abundance		750 mM

9 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 750 nM [U-13C; U-15N] PilE1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	PilE1	[U-13C; U-15N]		750 nM
2	Sodium Phosphate	natural abundance		750 mM
3	NaCl	natural abundance		750 mM

10 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6, Details 750 nM [U-13C; U-15N] PilE1, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	PilE1	[U-13C; U-15N]		750 nM
2	Sodium Phosphate	natural abundance		750 mM
3	NaCl	natural abundance		750 mM

NMR combined restraints 2 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts	combined_34325_6i2o.nef
Input source #2: Coordindates	6i2o.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	Error

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-----
HQDNARKSRIQSEHRELVSAIQSYIGAQDDPTNPSEITLAKLAPYMSKNAKNEDGIVNSLAKDKSGNSSTSAPGSAHQIDTTNHKLISTFTPSNGGQATV
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
HQDNARKSRIQSEHRELVSAIQSYIGAQDDPTNPSEITLAKLAPYMSKNAKNEDGIVNSLAKDKSGNSSTSAPGSAHQIDTTNHKLISTFTPSNGGQATV
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

--110--------
LTYDWSANGVNSN
|||||||||||||
LTYDWSANGVNSN
-------110---

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	113	0	0	100.0

Content subtype: combined_34325_6i2o.nef

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1204		100.0 (chain: A, length: 113)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 113, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 638
  - ¹³C chemical shifts: 460
  - ¹⁵N chemical shifts: 106
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Keywords PILIN, PILUS, PROTEIN FIBRIL, TYPE IV PILIN