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BMRB: 19151

2M6R

apo_YqcA

Authors

Jin, C., Hu, Y., Ye, Q.

Assembly

apo YqcA

Entity

1. apo YqcA (polymer), 149 monomers, 16282.99 Da Detail

MAEIGIFVGT MYGNSLLVAE EAEAILTAQG HKATVFEDPE LSDWLPYQDK YVLVVTSTTG QGDLPDSIVP LFQGIKDSLG FQPNLRYGVI ALGDSSYVNF CNGGKQFDAL LQEQSAQRVG EMLLIDASEN PEPETESNPW VEHWGTLLS

Formula weight

16282.99 Da

Source organism

Escherichia coli

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.0 %, Completeness: 88.6 %, Completeness (bb): 92.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	88.6 % (1498 of 1691)	88.0 % (764 of 868)	89.3 % (593 of 664)	88.7 % (141 of 159)
Backbone	92.7 % (814 of 878)	93.1 % (283 of 304)	93.8 % (406 of 433)	88.7 % (125 of 141)
Sidechain	85.7 % (812 of 948)	85.3 % (481 of 564)	86.1 % (315 of 366)	88.9 % (16 of 18)
Aromatic	50.7 % (73 of 144)	50.0 % (36 of 72)	49.3 % (34 of 69)	100.0 % (3 of 3)
Methyl	94.9 % (167 of 176)	94.3 % (83 of 88)	95.5 % (84 of 88)

1. entity

MAEIGIFVGT MYGNSLLVAE EAEAILTAQG HKATVFEDPE LSDWLPYQDK YVLVVTSTTG QGDLPDSIVP LFQGIKDSLG FQPNLRYGVI ALGDSSYVNF CNGGKQFDAL LQEQSAQRVG EMLLIDASEN PEPETESNPW VEHWGTLLS

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	protein	[U-15N]		1 mM
2	sodium phosphate	natural abundance		30 mM
3	DTT	natural abundance		20 mM
4	sodium chloride	natural abundance		30 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	protein	[U-13C; U-15N]		1 mM
8	sodium phosphate	natural abundance		30 mM
9	DTT	natural abundance		20 mM
10	sodium chloride	natural abundance		30 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2M6R, Strand ID: A Detail

Release date

2015-07-23

Citation

¹H, ¹³C and ¹⁵N resonance assignments of the apo and holo states of flavodoxin YqcA from Escherichia coli
Ye, Q., Hu, Y., Jin, C.
Biomol. NMR Assign. (2014), 8, 269-273, PubMed 23749454 , DOI 10.1007/s12104-013-9498-y , Abstract

Entries sharing articles BMRB: 2 entries Detail

  BMRB: 18154 released on 2014-04-21
    Title apo_YqcA
  BMRB: 19152 released on 2013-08-14
    Title holo_YqcA

Related entities 1. apo YqcA, : 1 : 1 : 2 : 142 entities Detail

Experiments performed 9 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 7.0

#	Name	Isotope labeling	Type	Concentration
1	protein	[U-15N]		1 mM
2	sodium phosphate	natural abundance		30 mM
3	DTT	natural abundance		20 mM
4	sodium chloride	natural abundance		30 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

2 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	protein	[U-13C; U-15N]		1 mM
8	sodium phosphate	natural abundance		30 mM
9	DTT	natural abundance		20 mM
10	sodium chloride	natural abundance		30 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

3 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	protein	[U-13C; U-15N]		1 mM
8	sodium phosphate	natural abundance		30 mM
9	DTT	natural abundance		20 mM
10	sodium chloride	natural abundance		30 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

4 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	protein	[U-13C; U-15N]		1 mM
8	sodium phosphate	natural abundance		30 mM
9	DTT	natural abundance		20 mM
10	sodium chloride	natural abundance		30 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

5 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 7.0

#	Name	Isotope labeling	Type	Concentration
7	protein	[U-13C; U-15N]		1 mM
8	sodium phosphate	natural abundance		30 mM
9	DTT	natural abundance		20 mM
10	sodium chloride	natural abundance		30 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

6 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	protein	[U-13C; U-15N]		1 mM
8	sodium phosphate	natural abundance		30 mM
9	DTT	natural abundance		20 mM
10	sodium chloride	natural abundance		30 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

7 3D HCCH-COSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	protein	[U-13C; U-15N]		1 mM
8	sodium phosphate	natural abundance		30 mM
9	DTT	natural abundance		20 mM
10	sodium chloride	natural abundance		30 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

8 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 7.0

#	Name	Isotope labeling	Type	Concentration
1	protein	[U-15N]		1 mM
2	sodium phosphate	natural abundance		30 mM
3	DTT	natural abundance		20 mM
4	sodium chloride	natural abundance		30 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

9 3D 1H-13C NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
7	protein	[U-13C; U-15N]		1 mM
8	sodium phosphate	natural abundance		30 mM
9	DTT	natural abundance		20 mM
10	sodium chloride	natural abundance		30 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_19151_2m6r.nef
Input source #2: Coordindates	2m6r.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
MAEIGIFVGTMYGNSLLVAEEAEAILTAQGHKATVFEDPELSDWLPYQDKYVLVVTSTTGQGDLPDSIVPLFQGIKDSLGFQPNLRYGVIALGDSSYVNF
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MAEIGIFVGTMYGNSLLVAEEAEAILTAQGHKATVFEDPELSDWLPYQDKYVLVVTSTTGQGDLPDSIVPLFQGIKDSLGFQPNLRYGVIALGDSSYVNF

-------110-------120-------130-------140---------
CNGGKQFDALLQEQSAQRVGEMLLIDASENPEPETESNPWVEHWGTLLS
|||||||||||||||||||||||||||||||||||||||||||||||||
CNGGKQFDALLQEQSAQRVGEMLLIDASENPEPETESNPWVEHWGTLLS

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	149	0	0	100.0

Content subtype: combined_19151_2m6r.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1485		96.0 (chain: A, length: 149)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	3838 (1)	undefined	95.3 (chain: A, length: 149)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 149, Sequence coverage: 96.0%
- Total number of assignments
  - ¹H chemical shifts: 760
  - ¹³C chemical shifts: 587
  - ¹⁵N chemical shifts: 138
- 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: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: undefined
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 149, Sequence coverage: 95.3%
- Total number of restraints: 3836
- Weight of restraints: 1.0 (3836)
- Potential type of restraints: upper-bound-parabolic (3836)
- Range of distance target values: 2.8, 7.0 (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

Keywords alpha/beta/alpha sandwich fold