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Found 1 Document (0.878 seconds)

BMRB: 30163

5T43

NMR Structure of Apo-form Human Tear Lipocalin

Authors

Vogel, H.J., Liu, Z.

Assembly

Lipocalin-1

Entity

1. Lipocalin-1 (polymer), 158 monomers, 17429.43 Da Detail

HHLLASDEEI QDVSGTWYLK AMTVDREFPE MNLESVTPMT LTTLEGGNLE AKVTMLISGR CQEVKAVLEK TDEPGKYTAD GGKHVAYIIR SHVKDHYIFY SEGELHGKPV RGVKLVGRDP KNNLEALEDF EKAAGARGLS TESILIPRQS ETCSPGSD

Formula weight

17429.43 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 84.8 %, Completeness: 26.6 %, Completeness (bb): 57.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹⁵N
All	26.6 % (289 of 1085)	16.7 % (155 of 926)	84.3 % (134 of 159)
Backbone	57.4 % (272 of 474)	42.7 % (138 of 323)	88.7 % (134 of 151)
Sidechain	2.8 % (17 of 611)	2.8 % (17 of 603)	0.0 % (0 of 8)
Aromatic	5.6 % (3 of 54)	5.7 % (3 of 53)	0.0 % (0 of 1)
Methyl	4.6 % (4 of 87)	4.6 % (4 of 87)

1. entity 1

HHLLASDEEI QDVSGTWYLK AMTVDREFPE MNLESVTPMT LTTLEGGNLE AKVTMLISGR CQEVKAVLEK TDEPGKYTAD GGKHVAYIIR SHVKDHYIFY SEGELHGKPV RGVKLVGRDP KNNLEALEDF EKAAGARGLS TESILIPRQS ETCSPGSD

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.4, Details 1.0 mM [U-99% 13C; U-99% 15N] Lipocalin, 90 % H2O, 10 % D2O, 50 mM sodium phosphate, 0.04 % sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	D2O	natural abundance	10 (±1.0) %
2	H2O	natural abundance	90 (±1.0) %
3	Lipocalin	[U-99% 13C; U-99% 15N]	1.0 (±0.1) mM
4	sodium azide	natural abundance	0.04 (±0.001) %
5	sodium phosphate	natural abundance	50 (±1.0) mM

Protein Blocks Logo

Calculated from 20 models in PDB: 5T43, Strand ID: A Detail

Release date

2016-11-10

Citation

NMR Structure of Apo-form Human Tear Lipocalin
Vogel, H.J., Liu, Z.

Related entities 1. Lipocalin-1, : 1 : 4 : 206 entities Detail

Interaction partners 1. Lipocalin-1, : 5 interactors Detail

More details for 5 interactors identified by 4 citations

Experiments performed 6 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 7.4, Details 1.0 mM [U-99% 13C; U-99% 15N] Lipocalin, 90 % H2O, 10 % D2O, 50 mM sodium phosphate, 0.04 % sodium azide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	D2O	natural abundance	10 (±1.0) %
2	H2O	natural abundance	90 (±1.0) %
3	Lipocalin	[U-99% 13C; U-99% 15N]	1.0 (±0.1) mM
4	sodium azide	natural abundance	0.04 (±0.001) %
5	sodium phosphate	natural abundance	50 (±1.0) mM

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	D2O	natural abundance	10 (±1.0) %
2	H2O	natural abundance	90 (±1.0) %
3	Lipocalin	[U-99% 13C; U-99% 15N]	1.0 (±0.1) mM
4	sodium azide	natural abundance	0.04 (±0.001) %
5	sodium phosphate	natural abundance	50 (±1.0) mM

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	D2O	natural abundance	10 (±1.0) %
2	H2O	natural abundance	90 (±1.0) %
3	Lipocalin	[U-99% 13C; U-99% 15N]	1.0 (±0.1) mM
4	sodium azide	natural abundance	0.04 (±0.001) %
5	sodium phosphate	natural abundance	50 (±1.0) mM

4 3D HNCACB

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	D2O	natural abundance	10 (±1.0) %
2	H2O	natural abundance	90 (±1.0) %
3	Lipocalin	[U-99% 13C; U-99% 15N]	1.0 (±0.1) mM
4	sodium azide	natural abundance	0.04 (±0.001) %
5	sodium phosphate	natural abundance	50 (±1.0) mM

5 3D HNCO

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	D2O	natural abundance	10 (±1.0) %
2	H2O	natural abundance	90 (±1.0) %
3	Lipocalin	[U-99% 13C; U-99% 15N]	1.0 (±0.1) mM
4	sodium azide	natural abundance	0.04 (±0.001) %
5	sodium phosphate	natural abundance	50 (±1.0) mM

6 3D HNCACO

Instrument

Bruker Avance - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	D2O	natural abundance	10 (±1.0) %
2	H2O	natural abundance	90 (±1.0) %
3	Lipocalin	[U-99% 13C; U-99% 15N]	1.0 (±0.1) mM
4	sodium azide	natural abundance	0.04 (±0.001) %
5	sodium phosphate	natural abundance	50 (±1.0) mM

NMR combined restraints 2 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts	combined_30163_5t43.nef
Input source #2: Coordindates	5t43.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Error

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:61:CYS:SG	A:153:CYS:SG	unknown	unknown	2.021

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
HHLLASDEEIQDVSGTWYLKAMTVDREFPEMNLESVTPMTLTTLEGGNLEAKVTMLISGRCQEVKAVLEKTDEPGKYTADGGKHVAYIIRSHVKDHYIFY
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
HHLLASDEEIQDVSGTWYLKAMTVDREFPEMNLESVTPMTLTTLEGGNLEAKVTMLISGRCQEVKAVLEKTDEPGKYTADGGKHVAYIIRSHVKDHYIFY

-------110-------120-------130-------140-------150--------
SEGELHGKPVRGVKLVGRDPKNNLEALEDFEKAAGARGLSTESILIPRQSETCSPGSD
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SEGELHGKPVRGVKLVGRDPKNNLEALEDFEKAAGARGLSTESILIPRQSETCSPGSD

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	158	0	0	100.0

Content subtype: combined_30163_5t43.nef

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	OK	264		83.5 (chain: A, length: 158)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 158, Sequence coverage: 83.5%
- Total number of assignments
  - ¹H chemical shifts: 132
  - ¹⁵N chemical shifts: 132
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	926	132	14.3
¹⁵N chemical shifts	166	132	79.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	323	132	40.9
¹⁵N chemical shifts	151	132	87.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	603	0	0.0
¹⁵N chemical shifts	15	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	91	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	53	0	0.0
¹⁵N chemical shifts	1	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Keywords TRANSPORT PROTEIN

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Found 1 Document (0.878 seconds)

BMRB: 30163

Sample

Related entities 1. Lipocalin-1, : 1 : 4 : 206 entities Detail

Interaction partners 1. Lipocalin-1, : 5 interactors Detail

Experiments performed 6 experiments Detail

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NMR combined restraints 2 contents Detail