BMRBj - BMREntryMaster

Found 1 Document (0.334 seconds)

BMRB: 30679

6UM9

Gypsy Moth Pheromone-binding protein 1 (LdisPBP1) NMR Structure at pH 4.5

Authors

Terrado, M., Plettner, E.

Assembly

Pheromone binding protein 1

Entity

1. Pheromone binding protein 1 (polymer, Thiol state: all disulfide bound), 143 monomers, 16145.74 Da Detail

SKEVMKQMTI NFAKPMEACK QELNVPDAVM QDFFNFWKEG YQITNREAGC VILCLAKKLE LLDQDMNLHH GKAMEFAMKH GADEAMAKQL LDIKHSCEKV ITIVADDPCQ TMLNLAMCFK AEIHKLDWAP TLDVAVGELL ADT

Formula weight

16145.74 Da

Entity Connection

disulfide 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS19:SG	1:CYS54:SG
2	disulfide	sing	1:CYS50:SG	1:CYS109:SG
3	disulfide	sing	1:CYS97:SG	1:CYS118:SG

Source organism

Lymantria dispar

Exptl. method

solution NMR

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 97.2 %, Completeness: 91.4 %, Completeness (bb): 93.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	91.4 % (1540 of 1685)	91.4 % (799 of 874)	90.5 % (594 of 656)	94.8 % (147 of 155)
Backbone	93.6 % (796 of 850)	93.0 % (267 of 287)	93.4 % (396 of 424)	95.7 % (133 of 139)
Sidechain	89.5 % (871 of 973)	90.6 % (532 of 587)	87.8 % (325 of 370)	87.5 % (14 of 16)
Aromatic	85.7 % (96 of 112)	85.7 % (48 of 56)	87.0 % (47 of 54)	50.0 % (1 of 2)
Methyl	92.1 % (151 of 164)	91.5 % (75 of 82)	92.7 % (76 of 82)

1. entity 1

SKEVMKQMTI NFAKPMEACK QELNVPDAVM QDFFNFWKEG YQITNREAGC VILCLAKKLE LLDQDMNLHH GKAMEFAMKH GADEAMAKQL LDIKHSCEKV ITIVADDPCQ TMLNLAMCFK AEIHKLDWAP TLDVAVGELL ADT

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 4.5, Details 1.2 M [U-99% 13C; U-99% 15N] LdisPBP1, 50 mM sodium acetate, 1 mM EDTA, 0.05 % w/v sodium azide, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	LdisPBP1	[U-99% 13C; U-99% 15N]	1.2 M
2	sodium acetate	natural abundance	50 mM
3	EDTA	natural abundance	1 mM
4	sodium azide	natural abundance	0.05 % w/v

Release date

2019-11-11

Citation

Ligand- and pH-Induced Structural Transition of Gypsy Moth Lymantria dispar Pheromone-Binding Protein 1 (LdisPBP1)
Terrado, M., Okon, M., McIntosh, L.P., Plettner, E.
Biochemistry (2020), 59, 3411-3426, PubMed 32877603 , DOI 10.1021/acs.biochem.0c00592 , Abstract

Related entities 1. Pheromone binding protein 1, : 1 : 44 entities Detail

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AVANCE III - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 4.5, Details 1.2 M [U-99% 13C; U-99% 15N] LdisPBP1, 50 mM sodium acetate, 1 mM EDTA, 0.05 % w/v sodium azide, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	LdisPBP1	[U-99% 13C; U-99% 15N]	1.2 M
2	sodium acetate	natural abundance	50 mM
3	EDTA	natural abundance	1 mM
4	sodium azide	natural abundance	0.05 % w/v

2 2D 1H-13C HSQC

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	LdisPBP1	[U-99% 13C; U-99% 15N]	1.2 M
2	sodium acetate	natural abundance	50 mM
3	EDTA	natural abundance	1 mM
4	sodium azide	natural abundance	0.05 % w/v

3 3D HNCACB

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	LdisPBP1	[U-99% 13C; U-99% 15N]	1.2 M
2	sodium acetate	natural abundance	50 mM
3	EDTA	natural abundance	1 mM
4	sodium azide	natural abundance	0.05 % w/v

4 3D CBCA(CO)NH

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	LdisPBP1	[U-99% 13C; U-99% 15N]	1.2 M
2	sodium acetate	natural abundance	50 mM
3	EDTA	natural abundance	1 mM
4	sodium azide	natural abundance	0.05 % w/v

5 3D HNCO

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	LdisPBP1	[U-99% 13C; U-99% 15N]	1.2 M
2	sodium acetate	natural abundance	50 mM
3	EDTA	natural abundance	1 mM
4	sodium azide	natural abundance	0.05 % w/v

6 3D HN(CO)CA

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	LdisPBP1	[U-99% 13C; U-99% 15N]	1.2 M
2	sodium acetate	natural abundance	50 mM
3	EDTA	natural abundance	1 mM
4	sodium azide	natural abundance	0.05 % w/v

7 3D C(CO)NH

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	LdisPBP1	[U-99% 13C; U-99% 15N]	1.2 M
2	sodium acetate	natural abundance	50 mM
3	EDTA	natural abundance	1 mM
4	sodium azide	natural abundance	0.05 % w/v

8 3D HBHA(CO)NH

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	LdisPBP1	[U-99% 13C; U-99% 15N]	1.2 M
2	sodium acetate	natural abundance	50 mM
3	EDTA	natural abundance	1 mM
4	sodium azide	natural abundance	0.05 % w/v

9 3D 1H-13C NOESY

Instrument

Bruker AVANCE III - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
1	LdisPBP1	[U-99% 13C; U-99% 15N]	1.2 M
2	sodium acetate	natural abundance	50 mM
3	EDTA	natural abundance	1 mM
4	sodium azide	natural abundance	0.05 % w/v

10 3D 1H-15N NOESY

Instrument

Bruker AVANCE III - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
1	LdisPBP1	[U-99% 13C; U-99% 15N]	1.2 M
2	sodium acetate	natural abundance	50 mM
3	EDTA	natural abundance	1 mM
4	sodium azide	natural abundance	0.05 % w/v

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30679_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)
1:19:CYS:SG	1:54:CYS:SG	oxidized, CA 60.271, CB 41.836 ppm	oxidized, CA 60.681, CB 43.218 ppm	n/a
1:50:CYS:SG	1:109:CYS:SG	oxidized, CA 55.489, CB 34.79 ppm	oxidized, CA 61.168, CB 44.504 ppm	n/a
1:97:CYS:SG	1:118:CYS:SG	oxidized, CA 59.847, CB 40.658 ppm	oxidized, CA 60.175, CB 38.651 ppm	n/a

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

None

Non-standard residues

None

Content subtype: bmr30679_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1746		97.2 (chain: 1, length: 143)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 143, Sequence coverage: 97.2%
- Total number of assignments
  - ¹H chemical shifts: 980
  - ¹³C chemical shifts: 610
  - ¹⁵N chemical shifts: 156
- Completeness of assignments
  - Entity_assemble_ID: 1
- 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: 1

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
69	HIS	ND1	183.026
69	HIS	NE2	171.918
70	HIS	ND1	177.988
70	HIS	NE2	172.696
80	HIS	ND1	176.412
80	HIS	NE2	173.746
95	HIS	ND1	177.035
95	HIS	NE2	176.05
124	HIS	ND1	176.767
124	HIS	NE2	175.808

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	874	822	94.1
¹³C chemical shifts	656	610	93.0
¹⁵N chemical shifts	155	146	94.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	287	274	95.5
¹³C chemical shifts	286	275	96.2
¹⁵N chemical shifts	139	132	95.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	587	548	93.4
¹³C chemical shifts	370	335	90.5
¹⁵N chemical shifts	16	14	87.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	92	79	85.9
¹³C chemical shifts	92	79	85.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	56	48	85.7
¹³C chemical shifts	54	47	87.0
¹⁵N chemical shifts	2	1	50.0

Keywords LIPID BINDING PROTEIN

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Found 1 Document (0.334 seconds)

BMRB: 30679

Sample

Related entities 1. Pheromone binding protein 1, : 1 : 44 entities Detail

Experiments performed 10 experiments Detail

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Chemical shift validation 3 contents Detail