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BMRB: 19152

2M6S

holo_YqcA

Authors

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

Assembly

holo YqcA

Entity

1. holo YqcA (polymer), 149 monomers, 16273.98 Da Detail

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

2. FLAVIN MONONUCLEOTIDE (non-polymer, Thiol state: not present), 456.344 Da

Total weight

16730.324 Da

Max. entity weight

16273.98 Da

Source organism

Escherichia coli

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.3 %, Completeness: 92.3 %, Completeness (bb): 97.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.3 % (1563 of 1693)	90.8 % (790 of 870)	93.2 % (618 of 663)	96.9 % (155 of 160)
Backbone	97.6 % (857 of 878)	97.0 % (295 of 304)	97.9 % (424 of 433)	97.9 % (138 of 141)
Sidechain	88.2 % (838 of 950)	87.5 % (495 of 566)	89.3 % (326 of 365)	89.5 % (17 of 19)
Aromatic	58.6 % (82 of 140)	57.1 % (40 of 70)	58.2 % (39 of 67)	100.0 % (3 of 3)
Methyl	94.9 % (167 of 176)	94.3 % (83 of 88)	95.5 % (84 of 88)

1. holo YqcA

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

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	holo_YqcA	[U-15N]		1 mM
2	sodium phosphate	natural abundance		30 mM
3	FLAVIN MONONUCLEOTIDE	natural abundance		50 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	holo_YqcA	[U-13C; U-15N]		1 mM
8	sodium phosphate	natural abundance		30 mM
9	FLAVIN MONONUCLEOTIDE	natural abundance		50 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: 2M6S, Strand ID: A Detail

Release date

2013-08-14

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: 19151 released on 2015-07-23
    Title apo_YqcA
  BMRB: 18154 released on 2014-04-21
    Title apo_YqcA

Related entities 1. holo YqcA, : 1 : 2 : 1 : 143 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	holo_YqcA	[U-15N]		1 mM
2	sodium phosphate	natural abundance		30 mM
3	FLAVIN MONONUCLEOTIDE	natural abundance		50 mM
4	sodium chloride	natural abundance		30 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

2 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	holo_YqcA	[U-13C; U-15N]		1 mM
8	sodium phosphate	natural abundance		30 mM
9	FLAVIN MONONUCLEOTIDE	natural abundance		50 mM
10	sodium chloride	natural abundance		30 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

3 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	holo_YqcA	[U-13C; U-15N]		1 mM
8	sodium phosphate	natural abundance		30 mM
9	FLAVIN MONONUCLEOTIDE	natural abundance		50 mM
10	sodium chloride	natural abundance		30 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

4 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	holo_YqcA	[U-13C; U-15N]		1 mM
8	sodium phosphate	natural abundance		30 mM
9	FLAVIN MONONUCLEOTIDE	natural abundance		50 mM
10	sodium chloride	natural abundance		30 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

5 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	holo_YqcA	[U-13C; U-15N]		1 mM
8	sodium phosphate	natural abundance		30 mM
9	FLAVIN MONONUCLEOTIDE	natural abundance		50 mM
10	sodium chloride	natural abundance		30 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

6 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	holo_YqcA	[U-13C; U-15N]		1 mM
8	sodium phosphate	natural abundance		30 mM
9	FLAVIN MONONUCLEOTIDE	natural abundance		50 mM
10	sodium chloride	natural abundance		30 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

7 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	holo_YqcA	[U-13C; U-15N]		1 mM
8	sodium phosphate	natural abundance		30 mM
9	FLAVIN MONONUCLEOTIDE	natural abundance		50 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	holo_YqcA	[U-15N]		1 mM
2	sodium phosphate	natural abundance		30 mM
3	FLAVIN MONONUCLEOTIDE	natural abundance		50 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	holo_YqcA	[U-13C; U-15N]		1 mM
8	sodium phosphate	natural abundance		30 mM
9	FLAVIN MONONUCLEOTIDE	natural abundance		50 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_19152_2m6s.nef
Input source #2: Coordindates	2m6s.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

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	FMN	FLAVIN MONONUCLEOTIDE	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_19152_2m6s.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Error	1590		98.7 (chain: A, length: 149)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	4902 (1)	noe	99.3 (chain: A, length: 149)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Error
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 149, Sequence coverage: 98.7%
- Total number of assignments
  - ¹H chemical shifts: 805
  - ¹³C chemical shifts: 627
  - ¹⁵N chemical shifts: 158
- Completeness of assignments
- 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: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 149, Sequence coverage: 99.3%
- Total number of restraints: 4889
- Weight of restraints: 1.0 (4889)
- Potential type of restraints: upper-bound-parabolic (4889)
- Range of distance target values: 2.2, 5.8 (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

Keywords alpha/beta/alpha sandwich fold