BMRBj - BMREntryMaster

Found 1 Document (0.714 seconds)

BMRB: 25028

2MQD

NMR structure of the hypotheical protein Lreu_0056 from Lactobacillus reuteri

Authors

Dutta, S.K., Serrano, P., Geralt, M., Wuthrich, K.

Assembly

NMR structure of the hypotheical protein Lreu 0056 from Lactobacillus reuteri

Entity

1. NMR structure of the hypotheical protein Lreu 0056 from Lactobacillus reuteri (polymer, Thiol state: all free), 119 monomers, 13270.91 Da Detail

GHMKFTDQQI GVLAGLAISP EWLKQNIAAN QLVYGIVKPS DTVPAGVDDY SYLVAADDQD GTIIFFKAEG QTVIIKYTSQ RNTKLKAKAL TLSQLKKEFY QTRSQKREVD DYVAGLRTE

Formula weight

13270.91 Da

Source organism

Limosilactobacillus reuteri

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 90.6 %, Completeness (bb): 83.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	90.6 % (1270 of 1401)	97.7 % (709 of 726)	80.0 % (436 of 545)	96.2 % (125 of 130)
Backbone	83.6 % (592 of 708)	97.5 % (237 of 243)	69.9 % (244 of 349)	95.7 % (111 of 116)
Sidechain	98.0 % (788 of 804)	97.7 % (472 of 483)	98.4 % (302 of 307)	100.0 % (14 of 14)
Aromatic	94.2 % (98 of 104)	94.2 % (49 of 52)	94.1 % (48 of 51)	100.0 % (1 of 1)
Methyl	100.0 % (148 of 148)	100.0 % (74 of 74)	100.0 % (74 of 74)

1. entity

GHMKFTDQQI GVLAGLAISP EWLKQNIAAN QLVYGIVKPS DTVPAGVDDY SYLVAADDQD GTIIFFKAEG QTVIIKYTSQ RNTKLKAKAL TLSQLKKEFY QTRSQKREVD DYVAGLRTE

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		5 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

LACS Plot; CA

Referencing offset: 0.24 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 0.24 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.11 ppm, Outliers: 5 Detail

Protein Blocks Logo

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

Release date

2014-09-01

Citation

NMR structure of the hypotheical protein Lreu_0056 from Lactobacillus reuteri
Dutta, S.K., Serrano, P., Geralt, M., Wuthrich, K.
Not known

Related entities 1. NMR structure of the hypotheical protein Lreu 0056 from Lactobacillus reuteri, : 1 : 1 entities Detail

Experiments performed 7 experiments Detail

1 APSY 4D-HACANH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		5 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

2 APSY 5D-HACACONH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		5 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

3 APSY 5D-CBCACONH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		5 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

4 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		5 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

5 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		5 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

6 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		5 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

7 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 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_25028_2mqd.nef
Input source #2: Coordindates	2mqd.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

-20-------30--------40--------50--------60--------70--------80--------90-------100-------110-------1
GHMKFTDQQIGVLAGLAISPEWLKQNIAANQLVYGIVKPSDTVPAGVDDYSYLVAADDQDGTIIFFKAEGQTVIIKYTSQRNTKLKAKALTLSQLKKEFY
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GHMKFTDQQIGVLAGLAISPEWLKQNIAANQLVYGIVKPSDTVPAGVDDYSYLVAADDQDGTIIFFKAEGQTVIIKYTSQRNTKLKAKALTLSQLKKEFY
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

20-------130-------
QTRSQKREVDDYVAGLRTE
|||||||||||||||||||
QTRSQKREVDDYVAGLRTE
-------110---------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	119	0	0	100.0

Content subtype: combined_25028_2mqd.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1255		100.0 (chain: A, length: 119)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	2376 (1)	noe	98.3 (chain: A, length: 119)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 119, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 709
  - ¹³C chemical shifts: 421
  - ¹⁵N chemical shifts: 125
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 119, Sequence coverage: 98.3%
- Total number of restraints: 2371
- Weight of restraints: 1.0 (2371)
- Potential type of restraints: upper-bound-parabolic (2371)
- Range of distance target values: 2.51, 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 human gut microbiome secreted protein, Protein of unknown function