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BMRB: 25158

2MTE

Solution structure of Doc48S

Authors

Chen, C., Feng, Y.

Assembly

Doc48S monomer

Entity

1. Doc48S monomer (polymer, Thiol state: not present), 69 monomers, 7660.438 Da Detail

STKLYGDVND DGKVNSTDAV ALKRYVLRSG ISINTDNADL NEDGRVNSTD LGILKRYILK EIDTLPYKN

Formula weight

7660.438 Da

Source organism

Acetivibrio thermocellus

Exptl. method

Refine. method

simulated annealing molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 97.7 %, Completeness (bb): 98.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	97.7 % (764 of 782)	96.3 % (390 of 405)	99.3 % (300 of 302)	98.7 % (74 of 75)
Backbone	98.5 % (406 of 412)	97.9 % (139 of 142)	99.0 % (200 of 202)	98.5 % (67 of 68)
Sidechain	97.2 % (422 of 434)	95.4 % (251 of 263)	100.0 % (164 of 164)	100.0 % (7 of 7)
Aromatic	100.0 % (32 of 32)	100.0 % (16 of 16)	100.0 % (16 of 16)
Methyl	100.0 % (88 of 88)	100.0 % (44 of 44)	100.0 % (44 of 44)

1. entity 1

STKLYGDVND DGKVNSTDAV ALKRYVLRSG ISINTDNADL NEDGRVNSTD LGILKRYILK EIDTLPYKN

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		0.3 ~ 0.5 mM
2	Bis-Tris	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	CaCl2	natural abundance		20 mM
5	DSS	natural abundance		0.02 % w/v
6	D2O	natural abundance		10 %
7	H2O	natural abundance		90 %

LACS Plot; CA

Referencing offset: 0.3 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 0.3 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.01 ppm, Outliers: 2 Detail

LACS Plot; CO

Referencing offset: 0.18 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2MTE, Strand ID: A Detail

Release date

2016-09-27

Citation

Revisiting the NMR solution structure of the Cel48S type-I dockerin module from Clostridium thermocellum reveals a cohesin-primed conformation
Chen, C., Cui, Z., Xiao, Y., Cui, Q., Smith, S.P., Lamed, R., Bayer, E.A., Feng, Y.
J. Struct. Biol. (2014), 188, 188-193, PubMed 25270376 , DOI 10.1016/j.jsb.2014.09.006 , Abstract

Related entities 1. Doc48S monomer, : 1 : 3 : 48 entities Detail

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		0.3 ~ 0.5 mM
2	Bis-Tris	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	CaCl2	natural abundance		20 mM
5	DSS	natural abundance		0.02 % w/v
6	D2O	natural abundance		10 %
7	H2O	natural abundance		90 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		0.3 ~ 0.5 mM
2	Bis-Tris	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	CaCl2	natural abundance		20 mM
5	DSS	natural abundance		0.02 % w/v
6	D2O	natural abundance		10 %
7	H2O	natural abundance		90 %

3 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		0.3 ~ 0.5 mM
2	Bis-Tris	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	CaCl2	natural abundance		20 mM
5	DSS	natural abundance		0.02 % w/v
6	D2O	natural abundance		10 %
7	H2O	natural abundance		90 %

4 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		0.3 ~ 0.5 mM
2	Bis-Tris	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	CaCl2	natural abundance		20 mM
5	DSS	natural abundance		0.02 % w/v
6	D2O	natural abundance		10 %
7	H2O	natural abundance		90 %

5 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		0.3 ~ 0.5 mM
2	Bis-Tris	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	CaCl2	natural abundance		20 mM
5	DSS	natural abundance		0.02 % w/v
6	D2O	natural abundance		10 %
7	H2O	natural abundance		90 %

6 3D HN(CA)CO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		0.3 ~ 0.5 mM
2	Bis-Tris	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	CaCl2	natural abundance		20 mM
5	DSS	natural abundance		0.02 % w/v
6	D2O	natural abundance		10 %
7	H2O	natural abundance		90 %

7 3D HBHA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		0.3 ~ 0.5 mM
2	Bis-Tris	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	CaCl2	natural abundance		20 mM
5	DSS	natural abundance		0.02 % w/v
6	D2O	natural abundance		10 %
7	H2O	natural abundance		90 %

8 3D HBHANH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		0.3 ~ 0.5 mM
2	Bis-Tris	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	CaCl2	natural abundance		20 mM
5	DSS	natural abundance		0.02 % w/v
6	D2O	natural abundance		10 %
7	H2O	natural abundance		90 %

9 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		0.3 ~ 0.5 mM
2	Bis-Tris	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	CaCl2	natural abundance		20 mM
5	DSS	natural abundance		0.02 % w/v
6	D2O	natural abundance		10 %
7	H2O	natural abundance		90 %

10 3D CCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		0.3 ~ 0.5 mM
2	Bis-Tris	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	CaCl2	natural abundance		20 mM
5	DSS	natural abundance		0.02 % w/v
6	D2O	natural abundance		10 %
7	H2O	natural abundance		90 %

11 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		0.3 ~ 0.5 mM
2	Bis-Tris	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	CaCl2	natural abundance		20 mM
5	DSS	natural abundance		0.02 % w/v
6	D2O	natural abundance		10 %
7	H2O	natural abundance		90 %

12 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		0.3 ~ 0.5 mM
2	Bis-Tris	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	CaCl2	natural abundance		20 mM
5	DSS	natural abundance		0.02 % w/v
6	D2O	natural abundance		10 %
7	H2O	natural abundance		90 %

13 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.6

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		0.3 ~ 0.5 mM
2	Bis-Tris	natural abundance		50 mM
3	potassium chloride	natural abundance		100 mM
4	CaCl2	natural abundance		20 mM
5	DSS	natural abundance		0.02 % w/v
6	D2O	natural abundance		10 %
7	H2O	natural abundance		90 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25158_2mte.nef
Input source #2: Coordindates	2mte.cif
Diamagnetism of the molecular assembly	False (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:43:ASP:OD2	2:2:CA:CA	unknown	unknown	n/a
1:50:ASP:OD1	2:2:CA:CA	unknown	unknown	n/a
1:50:ASP:OD2	2:2:CA:CA	unknown	unknown	n/a
1:13:LYS:O	2:1:CA:CA	unknown	unknown	n/a
1:7:ASP:OD1	2:1:CA:CA	unknown	unknown	n/a
1:39:ASP:OD1	2:2:CA:CA	unknown	unknown	n/a
1:18:ASP:OD1	2:1:CA:CA	unknown	unknown	n/a
1:9:ASN:OD1	2:1:CA:CA	unknown	unknown	n/a
1:18:ASP:OD2	2:1:CA:CA	unknown	unknown	n/a
1:11:ASP:OD2	2:1:CA:CA	unknown	unknown	n/a
1:41:ASN:OD1	2:2:CA:CA	unknown	unknown	n/a
1:45:ARG:O	2:2:CA:CA	unknown	unknown	n/a
1:43:ASP:OD1	2:2:CA:CA	unknown	unknown	n/a
1:11:ASP:OD1	2:1:CA:CA	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	CA	CALCIUM ION	None
B	2	CA	CALCIUM ION	None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40--------50--------60---------
STKLYGDVNDDGKVNSTDAVALKRYVLRSGISINTDNADLNEDGRVNSTDLGILKRYILKEIDTLPYKN
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
STKLYGDVNDDGKVNSTDAVALKRYVLRSGISINTDNADLNEDGRVNSTDLGILKRYILKEIDTLPYKN

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	69	0	0	100.0

Content subtype: combined_25158_2mte.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	14		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	775		100.0 (chain: A, length: 69)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	4258 (1)	noe	100.0 (chain: A, length: 69)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	36 (1)	hbond	40.6 (chain: A, length: 69)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_5	OK	122 (122)	.	98.6 (chain: A, length: 69)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 69, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 398
  - ¹³C chemical shifts: 299
  - ¹⁵N chemical shifts: 78
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: A

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 69, Sequence coverage: 100.0%
- Total number of restraints: 4183
- Weight of restraints: 1.0 (4183)
- Potential type of restraints: square-well-parabolic (4183)
- Range of distance target values: 2.3, 4.15 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 69, Sequence coverage: 40.6%
  - Total number of restraints: 36
  - Weight of restraints: 1.0 (36)
  - Potential type of restraints: square-well-parabolic (36)
  - Range of distance target values: 2.0, 3.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 69, Sequence coverage: 98.6%
- Total number of restraints: 122
- Total number of restraints per polymer type: 122
- Weight of restraints: 1.0 (122)
- Potential type of restraints: square-well-parabolic (122)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Calcium-binding protein