BMRBj - BMREntryMaster

	Total	¹H	¹³C	¹⁵N
All	80.4 % (986 of 1226)	88.1 % (560 of 636)	66.2 % (317 of 479)	98.2 % (109 of 111)
Backbone	80.5 % (512 of 636)	98.6 % (213 of 216)	62.3 % (198 of 318)	99.0 % (101 of 102)
Sidechain	81.9 % (567 of 692)	82.6 % (347 of 420)	80.6 % (212 of 263)	88.9 % (8 of 9)
Aromatic	46.4 % (26 of 56)	57.1 % (16 of 28)	33.3 % (9 of 27)	100.0 % (1 of 1)
Methyl	97.9 % (141 of 144)	97.2 % (70 of 72)	98.6 % (71 of 72)

1. entity 1

ALTTISPHDA QELIARGAKL IDIRDADEYL REHIPEADLA PLSVLEQSGL PAKLRHEQII FHCQAGKRTS NNADKLAAIA APAEIFLLED GIDGWKKAGL PVAVNKSQ

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 303 K, pH 7, Details 1 mM [U-99% 13C; U-99% 15N] Rhodanese domain, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Rhodanese domain	[U-99% 13C; U-99% 15N]		1 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 0.71 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 0.71 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 0.02 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 5LAM, Strand ID: A Detail

Release date

2016-08-14

Citation

S-Nitrosylation Induces Structural and Dynamical Changes in a Rhodanese Family Protein
Eichmann, C., Tzitzilonis, C., Nakamura, T., Kwiatkowski, W., Maslennikov, I., Choe, S., Lipton, S.A., Riek, R.
J. Mol. Biol. (2016), 428, 3737-3751, PubMed 27473602 , DOI 10.1016/j.jmb.2016.07.010 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 34010 released on 2016-08-14
Title S-nitrosylated 3D NMR structure of the cytoplasmic rhodanese domain of the inner membrane protein YgaP from Escherichia coli

Related entities 1. Inner membrane protein YgaP, : 1 : 5 : 5 : 63 entities Detail

Interaction partners 1. Inner membrane protein YgaP, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 6 experiments Detail

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_34009_5lam.nef
Input source #2: Coordindates	5lam.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
ALTTISPHDAQELIARGAKLIDIRDADEYLREHIPEADLAPLSVLEQSGLPAKLRHEQIIFHCQAGKRTSNNADKLAAIAAPAEIFLLEDGIDGWKKAGL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ALTTISPHDAQELIARGAKLIDIRDADEYLREHIPEADLAPLSVLEQSGLPAKLRHEQIIFHCQAGKRTSNNADKLAAIAAPAEIFLLEDGIDGWKKAGL

--------
PVAVNKSQ
||||||||
PVAVNKSQ

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	108	0	0	100.0

Content subtype: combined_34009_5lam.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	971		100.0 (chain: A, length: 108)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	2731 (1)	noe	97.2 (chain: A, length: 108)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 108, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 558
  - ¹³C chemical shifts: 303
  - ¹⁵N chemical shifts: 110
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
24	ARG	HH11	7.961
24	ARG	HH12	7.961
62	HIS	HD1	11.383
62	HIS	ND1	197.541
69	THR	HG1	1.906

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	636	553	86.9
¹³C chemical shifts	479	303	63.3
¹⁵N chemical shifts	116	109	94.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	216	210	97.2
¹³C chemical shifts	216	96	44.4
¹⁵N chemical shifts	102	100	98.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	420	343	81.7
¹³C chemical shifts	263	207	78.7
¹⁵N chemical shifts	14	9	64.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	72	70	97.2
¹³C chemical shifts	72	70	97.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	28	16	57.1
¹³C chemical shifts	27	9	33.3
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 108, Sequence coverage: 97.2%
- Total number of restraints: 2731
- Weight of restraints: 1.0 (2731)
- Potential type of restraints: upper-bound-parabolic (2731)
- Range of distance target values: 2.18, 5.7 (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 PROTEIN, Rhodanese domain of YgaP, membrane protein

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BMRB: 34009

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. Inner membrane protein YgaP, : 1 : 5 : 5 : 63 entities Detail

Interaction partners 1. Inner membrane protein YgaP, : 1 interactors Detail

Experiments performed 6 experiments Detail

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NMR combined restraints 3 contents Detail