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Found 1 Document (1.76 seconds)

BMRB: 4267

1NGL

Chemical shift assignments, 3JHNHA coupling constants and secondary structure of HNGAL (Human Neutrophil Gelatinase-Associated Lipocalin) in its apo form.

Authors

Coles, M., Diercks, T., Muehlenweg, B., Bartsch, S., Zoelzer, V., Tschesche, H., Kessler, H.

Assembly

apo-HNGAL Human Neutrophil Gelatinase-Associated Lipocalin

Entity

1. apo-HNGAL Human Neutrophil Gelatinase-Associated Lipocalin (polymer), 179 monomers, 20678.46 Da Detail

MQDSTSDLIP APPLSKVPLQ QNFQDNQFQG KWYVVGLAGN AILREDKDPQ KMYATIYELK EDKSYNVTSV LFRKKKCDYW IRTFVPGCQP GEFTLGNIKS YPGLTSYLVR VVSTNYNQHA MVFFKKVSQN REYFKITLYG RTKELTSELK ENFIRFSKSL GLPENHIVFP VPIDQCIDG

Formula weight

20678.46 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS77:SG	1:CYS176:SG

Source organism

Homo sapiens

Exptl. method

NMR

Refine. method

SIMULATED ANNEALING

Data set

assigned_chemical_shifts, coupling_constants, heteronucl_NOEs, heteronucl_T1_relaxation, heteronucl_T2_relaxation, order_parameters

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 90.5 %, Completeness (bb): 97.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	90.5 % (1994 of 2203)	92.8 % (1072 of 1155)	85.8 % (735 of 857)	97.9 % (187 of 191)
Backbone	97.4 % (1025 of 1052)	98.3 % (351 of 357)	96.4 % (508 of 527)	98.8 % (166 of 168)
Sidechain	86.0 % (1135 of 1320)	90.4 % (721 of 798)	78.8 % (393 of 499)	91.3 % (21 of 23)
Aromatic	68.0 % (151 of 222)	83.8 % (93 of 111)	51.4 % (56 of 109)	100.0 % (2 of 2)
Methyl	98.9 % (180 of 182)	98.9 % (90 of 91)	98.9 % (90 of 91)

1. HNGAL Human Neutrophil Gelatinase-Associated Lipocalin

MQDSTSDLIP APPLSKVPLQ QNFQDNQFQG KWYVVGLAGN AILREDKDPQ KMYATIYELK EDKSYNVTSV LFRKKKCDYW IRTFVPGCQP GEFTLGNIKS YPGLTSYLVR VVSTNYNQHA MVFFKKVSQN REYFKITLYG RTKELTSELK ENFIRFSKSL GLPENHIVFP VPIDQCIDG

Show sample condition

Sample

Temperature 298 K, pH 6.0, Details Uniformly 15N labelled sample, unliganded HNGAL.

#	Name	Isotope labeling	Concentration
1	HNGAL Human Neutrophil Gelatinase-Associated Lipocalin	[U-15N]	1.43 mM
2	sodium acetate		50 mM
3	acetic acid		50 mM
4	sodium chloride		50 mM
5	sodium azide		0.02 %
6	D2O		10.0 %
7	H2O		90.0 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	TMS	methyl protons	null	indirect	0.2514495
¹H	TMS	methyl protons	internal	direct	0.0
¹⁵N	TMS	methyl protons	null	indirect	0.1013291

Referencing offset: 0.27 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	TMS	methyl protons	null	indirect	0.2514495
¹H	TMS	methyl protons	internal	direct	0.0
¹⁵N	TMS	methyl protons	null	indirect	0.1013291

Referencing offset: 0.27 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	TMS	methyl protons	null	indirect	0.2514495
¹H	TMS	methyl protons	internal	direct	0.0
¹⁵N	TMS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.1 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	TMS	methyl protons	null	indirect	0.2514495
¹H	TMS	methyl protons	internal	direct	0.0
¹⁵N	TMS	methyl protons	null	indirect	0.1013291

Referencing offset: 0.58 ppm, Outliers: 6 Detail

Protein Blocks Logo

Calculated from 1 models in PDB: 1NGL, Strand ID: A Detail

Heteronucl. T₁

443 T₁ values in 3 lists
Coherence Sz, Field strength (¹H) 750 MHz, 500 MHz, 600 MHz, Temperature 298 K, pH 6.0 Detail

Heteronucl. T₂

445 T₂ values in 3 lists
Coherence S(+,-), Field strength (¹H) 750 MHz, 500 MHz, 600 MHz, Temperature 298 K, pH 6.0 Detail

Heteronucl. NOE

443 NOE values in 9 lists
Value type relative intensities, Field strength (¹H) 750 MHz, 500 MHz, 600 MHz, Temperature 298 K, pH 6.0 Detail

Heteronucl. T₁/T₂

442 T₁/T₂ values in 3 lists
Field strength (¹H) 750 MHz, 500 MHz, 600 MHz, Temperature 298 K, pH 6.0 Detail

Order parameters

152 S² values in 1 lists
Temperature 298 K, pH 6.0 Detail

Coupling constant

125 J values in 1 lists
Temperature 298 K, pH 6.0 Detail

Release date

2000-08-14

Citation

The Solution Strucuture and Dynamics of Human Neutrophil Gelatinase-associated Lipocalin
Coles, M., Diercks, T., Muehlenweg, B., Bartsch, S., Zoelzer, V., Tschesche, H., Kessler, H.
J. Mol. Biol. (1999), 289, 139-157, DOI 10.1006/jmbi.1999.2755

Related entities 1. apo-HNGAL Human Neutrophil Gelatinase-Associated Lipocalin, : 1 : 34 : 174 entities Detail

Interaction partners 1. apo-HNGAL Human Neutrophil Gelatinase-Associated Lipocalin, : 9 interactors Detail

More details for 9 interactors identified by 4 citations

Experiments performed 1 experiments Detail

#	Name	Isotope labeling	Concentration
8	HNGAL Human Neutrophil Gelatinase-Associated Lipocalin	[U-15N; U-13C]	1.15 mM
9	sodium acetate		50 mM
10	acetic acid		50 mM
11	sodium chloride		50 mM
12	sodium azide		0.02 %
13	D2O		10.0 %
14	H2O		90.0 %

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts, Heteronucl NOE exptl data, Heteronucl T1 relaxation data, Heteronucl T2 relaxation data, Order parameter relaxation analysis	bmr4267_3.str
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	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:77:CYS:SG	1:176:CYS:SG	oxidized, CA 52.87, CB 36.59 ppm	oxidized, CA 59.88, CB 36.5 ppm	n/a

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Content subtype: bmr4267_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts	Warning	2191		99.4 (chain: 1, length: 179)
1	Chemical shift references	chemical_shift_reference	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: 1, Chain length: 179, Sequence coverage: 99.4%

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
MQDSTSDLIPAPPLSKVPLQQNFQDNQFQGKWYVVGLAGNAILREDKDPQKMYATIYELKEDKSYNVTSVLFRKKKCDYWIRTFVPGCQPGEFTLGNIKS
||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||
MQDSTSDLIPAPPLSKVPLQQNFQDNQFQGKWYVVGLAGNAILREDKDP.KMYATIYELKEDKSYNVTSVLFRKKKCDYWIRTFVPGCQPGEFTLGNIKS

-------110-------120-------130-------140-------150-------160-------170---------
YPGLTSYLVRVVSTNYNQHAMVFFKKVSQNREYFKITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCIDG
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
YPGLTSYLVRVVSTNYNQHAMVFFKKVSQNREYFKITLYGRTKELTSELKENFIRFSKSLGLPENHIVFPVPIDQCIDG

Total number of assignments
- ¹H chemical shifts: 1266
- ¹³C chemical shifts: 737
- ¹⁵N chemical shifts: 188

Completeness of assignments

Entity_assemble_ID: 1

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
21	GLN	CD	180.46
22	ASN	CG	178.23
24	GLN	CD	180.56
26	ASN	CG	176.19
27	GLN	CD	178.95
29	GLN	CD	180.4
66	ASN	CG	175.52
89	GLN	CD	180.06
97	ASN	CG	178.66
117	ASN	CG	176.65
118	GLN	CD	180.58
129	GLN	CD	178.61
130	ASN	CG	178.61
141	ARG	HH11	5.82
141	ARG	HH12	5.82
141	ARG	HH21	4.59
141	ARG	HH22	4.59
152	ASN	CG	178.61
165	ASN	CG	178.61

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1155	1076	93.2
¹³C chemical shifts	857	722	84.2
¹⁵N chemical shifts	198	188	94.9

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	357	351	98.3
¹³C chemical shifts	358	335	93.6
¹⁵N chemical shifts	168	164	97.6

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	798	725	90.9
¹³C chemical shifts	499	387	77.6
¹⁵N chemical shifts	30	24	80.0

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	94	93	98.9
¹³C chemical shifts	94	93	98.9

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	111	93	83.8
¹³C chemical shifts	109	56	51.4
¹⁵N chemical shifts	2	2	100.0

Redox state of CYS
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: 1

Keywords coupling constants, lipocalin, NGAL, NMR, protein, resonance assignment, secondary structure

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Found 1 Document (1.76 seconds)

BMRB: 4267

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. apo-HNGAL Human Neutrophil Gelatinase-Associated Lipocalin, : 1 : 34 : 174 entities Detail

Interaction partners 1. apo-HNGAL Human Neutrophil Gelatinase-Associated Lipocalin, : 9 interactors Detail

Experiments performed 1 experiments Detail

Instrument

Sample #1

Sample #2

Chemical shift validation 3 contents Detail