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BMRB: 25454

2MYJ

Solution structure of a bacterial chaperone

Authors

Jin, C., Hu, Y., Ding, J.

Assembly

bacterial chaperone

Entity

1. bacterial chaperone (polymer, Thiol state: all disulfide bound), 79 monomers, 9065.140 × 2 Da Detail

ANESAKDMTC QEFIDLNPKA MTPVAWWMLH EETVYKGGDT VTLNETDLTQ IPKVIEYCKK NPQKNLYTFK NQASNDLPN

Total weight

18130.28 Da

Max. entity weight

9065.14 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS10:SG	1:CYS58:SG

Source organism

Escherichia coli

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 92.0 %, Completeness (bb): 97.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.0 % (867 of 942)	90.2 % (444 of 492)	93.1 % (337 of 362)	97.7 % (86 of 88)
Backbone	97.0 % (450 of 464)	98.1 % (152 of 155)	95.7 % (225 of 235)	98.6 % (73 of 74)
Sidechain	89.0 % (494 of 555)	86.6 % (292 of 337)	92.6 % (189 of 204)	92.9 % (13 of 14)
Aromatic	63.9 % (46 of 72)	63.9 % (23 of 36)	61.8 % (21 of 34)	100.0 % (2 of 2)
Methyl	93.6 % (73 of 78)	92.3 % (36 of 39)	94.9 % (37 of 39)

1. entity

ANESAKDMTC QEFIDLNPKA MTPVAWWMLH EETVYKGGDT VTLNETDLTQ IPKVIEYCKK NPQKNLYTFK NQASNDLPN

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		2.0 ~ 3.0 mM
2	entity_2	[U-13C; U-15N]		2.0 ~ 3.0 mM
3	sodium phosphate	natural abundance		50 mM
4	citric acid	natural abundance		45 mM
5	D2O	natural abundance		10 %
6	H2O	natural abundance		90 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
7	entity_1	[U-15N]		1.0 ~ 2.0 mM
8	entity_2	[U-15N]		1.0 ~ 2.0 mM
9	sodium phosphate	natural abundance		50 mM
10	citric acid	natural abundance		45 mM
11	D2O	natural abundance		10 %
12	H2O	natural abundance		90 %

Protein Blocks Logo

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

Release date

2016-01-03

Citation

HdeB chaperone activity is coupled to its intrinsic dynamic properties
Ding, J., Yang, C., Niu, X., Hu, Y., Jin, C.
Sci. Rep. (2015), 5, 16856-16856, PubMed 26593705 , DOI 10.1038/srep16856 , Abstract

Related entities 1. bacterial chaperone, : 2 : 3 entities Detail

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		2.0 ~ 3.0 mM
2	entity_2	[U-13C; U-15N]		2.0 ~ 3.0 mM
3	sodium phosphate	natural abundance		50 mM
4	citric acid	natural abundance		45 mM
5	D2O	natural abundance		10 %
6	H2O	natural abundance		90 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		2.0 ~ 3.0 mM
2	entity_2	[U-13C; U-15N]		2.0 ~ 3.0 mM
3	sodium phosphate	natural abundance		50 mM
4	citric acid	natural abundance		45 mM
5	D2O	natural abundance		10 %
6	H2O	natural abundance		90 %

3 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		2.0 ~ 3.0 mM
2	entity_2	[U-13C; U-15N]		2.0 ~ 3.0 mM
3	sodium phosphate	natural abundance		50 mM
4	citric acid	natural abundance		45 mM
5	D2O	natural abundance		10 %
6	H2O	natural abundance		90 %

4 3D CBCA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		2.0 ~ 3.0 mM
2	entity_2	[U-13C; U-15N]		2.0 ~ 3.0 mM
3	sodium phosphate	natural abundance		50 mM
4	citric acid	natural abundance		45 mM
5	D2O	natural abundance		10 %
6	H2O	natural abundance		90 %

5 3D HNCACB

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		2.0 ~ 3.0 mM
2	entity_2	[U-13C; U-15N]		2.0 ~ 3.0 mM
3	sodium phosphate	natural abundance		50 mM
4	citric acid	natural abundance		45 mM
5	D2O	natural abundance		10 %
6	H2O	natural abundance		90 %

6 3D HNCA

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		2.0 ~ 3.0 mM
2	entity_2	[U-13C; U-15N]		2.0 ~ 3.0 mM
3	sodium phosphate	natural abundance		50 mM
4	citric acid	natural abundance		45 mM
5	D2O	natural abundance		10 %
6	H2O	natural abundance		90 %

7 3D HN(CO)CA

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		2.0 ~ 3.0 mM
2	entity_2	[U-13C; U-15N]		2.0 ~ 3.0 mM
3	sodium phosphate	natural abundance		50 mM
4	citric acid	natural abundance		45 mM
5	D2O	natural abundance		10 %
6	H2O	natural abundance		90 %

8 3D HNCO

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		2.0 ~ 3.0 mM
2	entity_2	[U-13C; U-15N]		2.0 ~ 3.0 mM
3	sodium phosphate	natural abundance		50 mM
4	citric acid	natural abundance		45 mM
5	D2O	natural abundance		10 %
6	H2O	natural abundance		90 %

9 3D HCCH-COSY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		2.0 ~ 3.0 mM
2	entity_2	[U-13C; U-15N]		2.0 ~ 3.0 mM
3	sodium phosphate	natural abundance		50 mM
4	citric acid	natural abundance		45 mM
5	D2O	natural abundance		10 %
6	H2O	natural abundance		90 %

10 3D 1H-15N NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		2.0 ~ 3.0 mM
2	entity_2	[U-13C; U-15N]		2.0 ~ 3.0 mM
3	sodium phosphate	natural abundance		50 mM
4	citric acid	natural abundance		45 mM
5	D2O	natural abundance		10 %
6	H2O	natural abundance		90 %

11 3D 1H-13C NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		2.0 ~ 3.0 mM
2	entity_2	[U-13C; U-15N]		2.0 ~ 3.0 mM
3	sodium phosphate	natural abundance		50 mM
4	citric acid	natural abundance		45 mM
5	D2O	natural abundance		10 %
6	H2O	natural abundance		90 %

12 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		2.0 ~ 3.0 mM
2	entity_2	[U-13C; U-15N]		2.0 ~ 3.0 mM
3	sodium phosphate	natural abundance		50 mM
4	citric acid	natural abundance		45 mM
5	D2O	natural abundance		10 %
6	H2O	natural abundance		90 %

13 3D (H)CCH-TOCSY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-13C; U-15N]		2.0 ~ 3.0 mM
2	entity_2	[U-13C; U-15N]		2.0 ~ 3.0 mM
3	sodium phosphate	natural abundance		50 mM
4	citric acid	natural abundance		45 mM
5	D2O	natural abundance		10 %
6	H2O	natural abundance		90 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_25454_2myj.nef
Input source #2: Coordindates	2myj.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:10:CYS:SG	A:58:CYS:SG	reduced, CA 56.97, CB 32.44 ppm	reduced, CA 52.02, CB 31.667 ppm	2.051
B:89:CYS:SG	B:137:CYS:SG	unknown	unknown	2.047

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---------
ANESAKDMTCQEFIDLNPKAMTPVAWWMLHEETVYKGGDTVTLNETDLTQIPKVIEYCKKNPQKNLYTFKNQASNDLPN
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ANESAKDMTCQEFIDLNPKAMTPVAWWMLHEETVYKGGDTVTLNETDLTQIPKVIEYCKKNPQKNLYTFKNQASNDLPN

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

80-------90-------100-------110-------120-------130-------140-------150--------
ANESAKDMTCQEFIDLNPKAMTPVAWWMLHEETVYKGGDTVTLNETDLTQIPKVIEYCKKNPQKNLYTFKNQASNDLPN
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ANESAKDMTCQEFIDLNPKAMTPVAWWMLHEETVYKGGDTVTLNETDLTQIPKVIEYCKKNPQKNLYTFKNQASNDLPN
--------10--------20--------30--------40--------50--------60--------70---------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	79	0	0	100.0
B	B	79	0	0	100.0

Content subtype: combined_25454_2myj.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	867		100.0 (chain: A, length: 79)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	3974 (1)	noe	100.0 (chain: A, length: 79), 100.0 (chain: B, length: 79)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	20 (1)	noe	10.1 (chain: A, length: 79), 10.1 (chain: B, length: 79)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 79, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 444
  - ¹³C chemical shifts: 337
  - ¹⁵N chemical shifts: 86
- 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

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 79, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 79, Sequence coverage: 100.0%
- Total number of restraints: 3957
- Weight of restraints: 1.0 (3957)
- Potential type of restraints: upper-bound-parabolic (3957)
- Range of distance target values: 2.8, 5.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_3
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 79, Sequence coverage: 10.1%
    - Entity_assembly_ID: B, Chain length: 79, Sequence coverage: 10.1%
  - Total number of restraints: 20
  - Weight of restraints: 1.0 (20)
  - Potential type of restraints: upper-bound-parabolic (20)
  - Range of distance target values: 3.5, 5.5 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map

Keywords dimer, protein