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BMRB: 17799

2LG7

NMR structure of the protein YP_001302112.1 from Parabacteroides distasonis

Authors

Serrano, P., Mohanty, B., Geralt, M., Wuthrich, K.

Assembly

YP 001302112.1

Entity

1. YP 001302112.1 (polymer, Thiol state: all free), 200 monomers, 21926.54 Da Detail

MRKYLYLSAV CVCMALCFVG CSKDDDEPGG KGAMYEVTIE QSGDFRSFIK SVVVVANGTQ LKDGATGESL ASPVILSDEE LAVEKVTLST TGKAIEFAVS GGVVDGEDGV VNEPMQWVVT VYKNGKEIEK KSLVFRDGKE ISTDDLNLYY NVVDGEDGVV NEPMQWVVTV YKNGKEIEKK SLVFRDGKEI STDDLNLYYN

Formula weight

21926.54 Da

Source organism

Parabacteroides distasonis

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 68.0 %, Completeness: 63.1 %, Completeness (bb): 64.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	63.1 % (1428 of 2262)	63.2 % (735 of 1163)	62.3 % (553 of 888)	66.4 % (140 of 211)
Backbone	64.6 % (770 of 1192)	65.3 % (271 of 415)	63.5 % (369 of 581)	66.3 % (130 of 196)
Sidechain	62.4 % (781 of 1251)	62.0 % (464 of 748)	62.9 % (307 of 488)	66.7 % (10 of 15)
Aromatic	46.2 % (72 of 156)	46.2 % (36 of 78)	46.1 % (35 of 76)	50.0 % (1 of 2)
Methyl	62.6 % (149 of 238)	62.2 % (74 of 119)	63.0 % (75 of 119)

1. entity

MRKYLYLSAV CVCMALCFVG CSKDDDEPGG KGAMYEVTIE QSGDFRSFIK SVVVVANGTQ LKDGATGESL ASPVILSDEE LAVEKVTLST TGKAIEFAVS GGVVDGEDGV VNEPMQWVVT VYKNGKEIEK KSLVFRDGKE ISTDDLNLYY NVVDGEDGVV NEPMQWVVTV YKNGKEIEKK SLVFRDGKEI STDDLNLYYN

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	YP_001302112	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		25 mM
4	sodium azide	natural abundance		5 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

LACS Plot; CA

Referencing offset: 2.57 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 2.57 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.09 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 3.27 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2LG7, Strand ID: A Detail

Release date

2011-08-24

Citation

NMR structure of the protein YP_001302112.1 from Parabacteroides distasonis
Serrano, P., Mohanty, B., Geralt, M., Wuthrich, K.
Not known

Experiments performed 7 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	YP_001302112	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		25 mM
4	sodium azide	natural abundance		5 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

2 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	YP_001302112	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		25 mM
4	sodium azide	natural abundance		5 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

3 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	YP_001302112	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		25 mM
4	sodium azide	natural abundance		5 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

4 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	YP_001302112	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		25 mM
4	sodium azide	natural abundance		5 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

5 5D APSY CBCACONH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	YP_001302112	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		25 mM
4	sodium azide	natural abundance		5 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

6 4D APSY HACANH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	YP_001302112	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		25 mM
4	sodium azide	natural abundance		5 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

7 5D APSY HACACONH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	YP_001302112	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		25 mM
4	sodium azide	natural abundance		5 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_17799_2lg7.nef
Input source #2: Coordindates	2lg7.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

None

Sequence alignments

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

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
GDDDEPGGKGAMYEVTIEQSGDFRSFIKSVVVVANGTQLKDGATGESLASPVILSDEELAVEKVTLSTTGKAIEFAVSGGVVDGEDGVVNEPMQWVVTVY
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GDDDEPGGKGAMYEVTIEQSGDFRSFIKSVVVVANGTQLKDGATGESLASPVILSDEELAVEKVTLSTTGKAIEFAVSGGVVDGEDGVVNEPMQWVVTVY

-------110-------120---------
KNGKEIEKKSLVFRDGKEISTDDLNLYYN
|||||||||||||||||||||||||||||
KNGKEIEKKSLVFRDGKEISTDDLNLYYN

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	129	0	0	100.0

Content subtype: combined_17799_2lg7.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Error	1262		93.8 (chain: A, length: 129)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	2127 (1)	noe	93.0 (chain: A, length: 129)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Error
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 129, Sequence coverage: 93.8%
- Total number of assignments
  - ¹H chemical shifts: 650
  - ¹³C chemical shifts: 488
  - ¹⁵N chemical shifts: 124
- Completeness of assignments
- 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

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 129, Sequence coverage: 93.0%
- Total number of restraints: 2127
- Weight of restraints: 1.0 (2127)
- Potential type of restraints: upper-bound-parabolic (2127)
- Range of distance target values: 2.65, 5.5 (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 APSY spectroscopy, Parabacteroides distasonis