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BMRB: 30926

6V9Z

Solution NMR structure of peptidase domain from Clostridium thermocellum PCAT1

Authors

Bhattacharya, S., Palillo, A.

Assembly

ABC-type bacteriocin transporter

Entity

1. ABC-type bacteriocin transporter (polymer), 151 monomers, 16612.19 Da Detail

SNAMLRRLFK KKYVCVRQYD LTDAGAACLS SIAQYYGLKM SLAKIREMTG TDTQGTNAYG LIHAAKQLGF SAKGVKASKE DLLKDFRLPA IANVIVDNRL AHFVVIYSIK NRIITVADPG KGIVRYSMDD FCSIWTGGLV LLEPGEAFQK G

Formula weight

16612.19 Da

Source organism

Acetivibrio thermocellus ATCC 27405

Exptl. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.4 %, Completeness: 93.1 %, Completeness (bb): 94.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	93.1 % (1643 of 1765)	95.2 % (864 of 908)	90.7 % (626 of 690)	91.6 % (153 of 167)
Backbone	94.4 % (850 of 900)	96.5 % (301 of 312)	92.7 % (408 of 440)	95.3 % (141 of 148)
Sidechain	92.3 % (926 of 1003)	94.5 % (563 of 596)	90.5 % (351 of 388)	63.2 % (12 of 19)
Aromatic	75.0 % (102 of 136)	89.7 % (61 of 68)	59.7 % (40 of 67)	100.0 % (1 of 1)
Methyl	97.9 % (186 of 190)	97.9 % (93 of 95)	97.9 % (93 of 95)

1. entity 1

SNAMLRRLFK KKYVCVRQYD LTDAGAACLS SIAQYYGLKM SLAKIREMTG TDTQGTNAYG LIHAAKQLGF SAKGVKASKE DLLKDFRLPA IANVIVDNRL AHFVVIYSIK NRIITVADPG KGIVRYSMDD FCSIWTGGLV LLEPGEAFQK G

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 7.0, Details 675 uM [U-100% 13C; U-100% 15N] C39 peptidase domain, 50 uM sodium phosphate, 150 uM sodium chloride, 5 mM DTT, 50 mM PBS buffer, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	C39 peptidase domain	[U-100% 13C; U-100% 15N]		675 uM
2	sodium phosphate	natural abundance		50 uM
3	sodium chloride	natural abundance		150 uM
4	DTT	natural abundance		5 mM
5	PBS buffer	natural abundance		50 mM

Release date

2021-06-17

Citation

Structural and dynamic studies of the peptidase domain from Clostridium thermocellum PCAT1
Bhattacharya, S., Pallilo, A.
Protein Sci. (2022), 31, 498-512, PubMed 34865273 , DOI 10.1002/pro.4248 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 30950 released on 2021-10-10
Title Solution NMR structure of substrate bound peptidase domain from PCAT1

Related entities 1. ABC-type bacteriocin transporter, : 1 : 2 : 6 : 33 entities Detail

Experiments performed 15 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AVANCE III HD - 800 MHz TCI CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 7.0, Details 675 uM [U-100% 13C; U-100% 15N] C39 peptidase domain, 50 uM sodium phosphate, 150 uM sodium chloride, 5 mM DTT, 50 mM PBS buffer, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	C39 peptidase domain	[U-100% 13C; U-100% 15N]		675 uM
2	sodium phosphate	natural abundance		50 uM
3	sodium chloride	natural abundance		150 uM
4	DTT	natural abundance		5 mM
5	PBS buffer	natural abundance		50 mM

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker AVANCE III HD - 800 MHz TCI CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 7.0, Details 675 uM [U-100% 13C; U-100% 15N] C39 peptidase domain, 50 uM sodium phosphate, 150 uM sodium chloride, 5 mM DTT, 50 mM PBS buffer, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	C39 peptidase domain	[U-100% 13C; U-100% 15N]		675 uM
2	sodium phosphate	natural abundance		50 uM
3	sodium chloride	natural abundance		150 uM
4	DTT	natural abundance		5 mM
5	PBS buffer	natural abundance		50 mM

3 2D 1H-13C HSQC aromatic

Instrument

Bruker AVANCE III HD - 800 MHz TCI CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 7.0, Details 675 uM [U-100% 13C; U-100% 15N] C39 peptidase domain, 50 uM sodium phosphate, 150 uM sodium chloride, 5 mM DTT, 50 mM PBS buffer, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	C39 peptidase domain	[U-100% 13C; U-100% 15N]		675 uM
2	sodium phosphate	natural abundance		50 uM
3	sodium chloride	natural abundance		150 uM
4	DTT	natural abundance		5 mM
5	PBS buffer	natural abundance		50 mM

4 3D HNCO

Instrument

Bruker AVANCE III HD - 800 MHz TCI CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 7.0, Details 675 uM [U-100% 13C; U-100% 15N] C39 peptidase domain, 50 uM sodium phosphate, 150 uM sodium chloride, 5 mM DTT, 50 mM PBS buffer, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	C39 peptidase domain	[U-100% 13C; U-100% 15N]		675 uM
2	sodium phosphate	natural abundance		50 uM
3	sodium chloride	natural abundance		150 uM
4	DTT	natural abundance		5 mM
5	PBS buffer	natural abundance		50 mM

5 3D HNCA

Instrument

Bruker AVANCE III HD - 800 MHz TCI CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 7.0, Details 675 uM [U-100% 13C; U-100% 15N] C39 peptidase domain, 50 uM sodium phosphate, 150 uM sodium chloride, 5 mM DTT, 50 mM PBS buffer, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	C39 peptidase domain	[U-100% 13C; U-100% 15N]		675 uM
2	sodium phosphate	natural abundance		50 uM
3	sodium chloride	natural abundance		150 uM
4	DTT	natural abundance		5 mM
5	PBS buffer	natural abundance		50 mM

6 3D HCCH-TOCSY

Instrument

Bruker AVANCE III HD - 800 MHz TCI CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 7.0, Details 675 uM [U-100% 13C; U-100% 15N] C39 peptidase domain, 50 uM sodium phosphate, 150 uM sodium chloride, 5 mM DTT, 50 mM PBS buffer, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	C39 peptidase domain	[U-100% 13C; U-100% 15N]		675 uM
2	sodium phosphate	natural abundance		50 uM
3	sodium chloride	natural abundance		150 uM
4	DTT	natural abundance		5 mM
5	PBS buffer	natural abundance		50 mM

7 3D HBHA(CO)NH

Instrument

Bruker AVANCE III HD - 800 MHz TCI CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 7.0, Details 675 uM [U-100% 13C; U-100% 15N] C39 peptidase domain, 50 uM sodium phosphate, 150 uM sodium chloride, 5 mM DTT, 50 mM PBS buffer, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	C39 peptidase domain	[U-100% 13C; U-100% 15N]		675 uM
2	sodium phosphate	natural abundance		50 uM
3	sodium chloride	natural abundance		150 uM
4	DTT	natural abundance		5 mM
5	PBS buffer	natural abundance		50 mM

8 3D HN(CO)CA

Instrument

Bruker AVANCE III HD - 800 MHz TCI CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 7.0, Details 675 uM [U-100% 13C; U-100% 15N] C39 peptidase domain, 50 uM sodium phosphate, 150 uM sodium chloride, 5 mM DTT, 50 mM PBS buffer, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	C39 peptidase domain	[U-100% 13C; U-100% 15N]		675 uM
2	sodium phosphate	natural abundance		50 uM
3	sodium chloride	natural abundance		150 uM
4	DTT	natural abundance		5 mM
5	PBS buffer	natural abundance		50 mM

9 3D HNCACB

Instrument

Bruker AVANCE III HD - 800 MHz TCI CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 7.0, Details 675 uM [U-100% 13C; U-100% 15N] C39 peptidase domain, 50 uM sodium phosphate, 150 uM sodium chloride, 5 mM DTT, 50 mM PBS buffer, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	C39 peptidase domain	[U-100% 13C; U-100% 15N]		675 uM
2	sodium phosphate	natural abundance		50 uM
3	sodium chloride	natural abundance		150 uM
4	DTT	natural abundance		5 mM
5	PBS buffer	natural abundance		50 mM

10 3D CBCA(CO)NH

Instrument

Bruker AVANCE III HD - 800 MHz TCI CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 7.0, Details 675 uM [U-100% 13C; U-100% 15N] C39 peptidase domain, 50 uM sodium phosphate, 150 uM sodium chloride, 5 mM DTT, 50 mM PBS buffer, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	C39 peptidase domain	[U-100% 13C; U-100% 15N]		675 uM
2	sodium phosphate	natural abundance		50 uM
3	sodium chloride	natural abundance		150 uM
4	DTT	natural abundance		5 mM
5	PBS buffer	natural abundance		50 mM

11 3D H(CCO)NH

Instrument

Bruker AVANCE III HD - 800 MHz TCI CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 7.0, Details 675 uM [U-100% 13C; U-100% 15N] C39 peptidase domain, 50 uM sodium phosphate, 150 uM sodium chloride, 5 mM DTT, 50 mM PBS buffer, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	C39 peptidase domain	[U-100% 13C; U-100% 15N]		675 uM
2	sodium phosphate	natural abundance		50 uM
3	sodium chloride	natural abundance		150 uM
4	DTT	natural abundance		5 mM
5	PBS buffer	natural abundance		50 mM

12 3D C(CO)NH

Instrument

Bruker AVANCE III HD - 800 MHz TCI CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 7.0, Details 675 uM [U-100% 13C; U-100% 15N] C39 peptidase domain, 50 uM sodium phosphate, 150 uM sodium chloride, 5 mM DTT, 50 mM PBS buffer, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	C39 peptidase domain	[U-100% 13C; U-100% 15N]		675 uM
2	sodium phosphate	natural abundance		50 uM
3	sodium chloride	natural abundance		150 uM
4	DTT	natural abundance		5 mM
5	PBS buffer	natural abundance		50 mM

13 3D 1H-13C NOESY aromatic

Instrument

Bruker AVANCE - na MHz TCI CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 7.0, Details 675 uM [U-100% 13C; U-100% 15N] C39 peptidase domain, 50 uM sodium phosphate, 150 uM sodium chloride, 5 mM DTT, 50 mM PBS buffer, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	C39 peptidase domain	[U-100% 13C; U-100% 15N]		675 uM
2	sodium phosphate	natural abundance		50 uM
3	sodium chloride	natural abundance		150 uM
4	DTT	natural abundance		5 mM
5	PBS buffer	natural abundance		50 mM

14 3D 1H-13C NOESY aliphatic

Instrument

Bruker AVANCE - na MHz TCI CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 7.0, Details 675 uM [U-100% 13C; U-100% 15N] C39 peptidase domain, 50 uM sodium phosphate, 150 uM sodium chloride, 5 mM DTT, 50 mM PBS buffer, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	C39 peptidase domain	[U-100% 13C; U-100% 15N]		675 uM
2	sodium phosphate	natural abundance		50 uM
3	sodium chloride	natural abundance		150 uM
4	DTT	natural abundance		5 mM
5	PBS buffer	natural abundance		50 mM

15 3D 1H-15N NOESY

Instrument

Bruker AVANCE - na MHz TCI CryoProbe

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 7.0, Details 675 uM [U-100% 13C; U-100% 15N] C39 peptidase domain, 50 uM sodium phosphate, 150 uM sodium chloride, 5 mM DTT, 50 mM PBS buffer, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	C39 peptidase domain	[U-100% 13C; U-100% 15N]		675 uM
2	sodium phosphate	natural abundance		50 uM
3	sodium chloride	natural abundance		150 uM
4	DTT	natural abundance		5 mM
5	PBS buffer	natural abundance		50 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30926_3.str
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

Content subtype: bmr30926_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1830		97.4 (chain: 1, length: 151)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 151, Sequence coverage: 97.4%
- Total number of assignments
  - ¹H chemical shifts: 1057
  - ¹³C chemical shifts: 622
  - ¹⁵N chemical shifts: 151
- Completeness of assignments
  - Entity_assemble_ID: 1
- 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: 1

Keywords C39 peptidase domain, PEPTIDE BINDING PROTEIN