BMRBj - BMREntryMaster

Found 1 Document (0.515 seconds)

BMRB: 16021

2RQF

NMR assignments of juvenile hormone binding protein in complex with JH III

Authors

Tase, A., Fujimoto, Z., Shiotsuki, T.

Assembly

hJHBP

Entity

1. hJHBP (polymer, Thiol state: free and disulfide bound), 227 monomers, 24756.85 Da Detail

GSDGDALLKP CKLGDMQCLS SATEQFLEKT SKGIPQYDIW PIDPLVVTSL DVIAPSDAGI VIRFKNLNIT GLKNQQISDF QMDTKAKTVL LKTKADLHIV GDIVIELTEQ SKSFTGLYTA DTNVIGAVRY GYNLKNDDNG VQHFEVQPET FTCESIGEPK ITLSSDLSSA LEKDSGNNSL EPDMEPLKTL RQAAICKIAE ACYISVVHNI RASAKILPAS SFFENLN

Formula weight

24756.85 Da

Entity Connection

disulfide 2 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS11:SG	1:CYS18:SG
2	disulfide	sing	1:CYS153:SG	1:CYS196:SG

Source organism

Bombyx mori

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 98.2 %, Completeness (bb): 98.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	98.2 % (2548 of 2595)	97.5 % (1307 of 1341)	99.0 % (1004 of 1014)	98.8 % (237 of 240)
Backbone	98.3 % (1319 of 1342)	97.4 % (445 of 457)	99.0 % (661 of 668)	98.2 % (213 of 217)
Sidechain	96.9 % (1422 of 1467)	96.5 % (853 of 884)	97.5 % (546 of 560)	100.0 % (23 of 23)
Aromatic	91.7 % (132 of 144)	91.7 % (66 of 72)	91.5 % (65 of 71)	100.0 % (1 of 1)
Methyl	98.2 % (277 of 282)	97.9 % (138 of 141)	98.6 % (139 of 141)

1. hJHBP

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.0

#	Name	Isotope labeling	Concentration
1	hJHBP	[U-15N]	0.6-1.0 mM
2	JH III	natural abundance	0.6-1.0 mM
3	sodium phosphate	natural abundance	45 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.0

#	Name	Isotope labeling	Concentration
6	hJHBP	[U-13C; U-15N]	0.6-1.0 mM
7	JH III	natural abundance	0.6-1.0 mM
8	sodium phosphate	natural abundance	45 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.0

#	Name	Isotope labeling	Concentration
11	hJHBP	[U-13C; U-15N]	0.6-1.0 mM
12	JH III	natural abundance	0.6-1.0 mM
13	sodium phosphate	natural abundance	45 mM
14	D2O	natural abundance	100 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	TSP	methyl carbons	external	direct	1.0
¹H	TSP	methyl protons	external	direct	1.0
¹⁵N	ammonium hydroxide	nitrogen	external	direct	1.0

Referencing offset: 0.02 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	TSP	methyl carbons	external	direct	1.0
¹H	TSP	methyl protons	external	direct	1.0
¹⁵N	ammonium hydroxide	nitrogen	external	direct	1.0

Referencing offset: 0.02 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	TSP	methyl carbons	external	direct	1.0
¹H	TSP	methyl protons	external	direct	1.0
¹⁵N	ammonium hydroxide	nitrogen	external	direct	1.0

Referencing offset: -0.16 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	TSP	methyl carbons	external	direct	1.0
¹H	TSP	methyl protons	external	direct	1.0
¹⁵N	ammonium hydroxide	nitrogen	external	direct	1.0

Referencing offset: 0.29 ppm, Outliers: 3 Detail

Release date

2009-01-27

Citation

NMR assignments of juvenile hormone binding protein in complex with JH III
Suzuki, R., Tase, A., Fujimoto, Z., Shiotsuki, T., Yamazaki, T.
Biomol. NMR Assign. (2009), 3, 73-76, PubMed 19636950 , DOI 10.1007/s12104-009-9144-x , Abstract

Related entities 1. hJHBP, : 1 : 3 : 3 entities Detail

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.0

#	Name	Isotope labeling	Concentration
1	hJHBP	[U-15N]	0.6-1.0 mM
2	JH III	natural abundance	0.6-1.0 mM
3	sodium phosphate	natural abundance	45 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

2 2D 1H-13C HSQC

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.0

#	Name	Isotope labeling	Concentration
11	hJHBP	[U-13C; U-15N]	0.6-1.0 mM
12	JH III	natural abundance	0.6-1.0 mM
13	sodium phosphate	natural abundance	45 mM
14	D2O	natural abundance	100 %

3 3D HNCO

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.0

#	Name	Isotope labeling	Concentration
6	hJHBP	[U-13C; U-15N]	0.6-1.0 mM
7	JH III	natural abundance	0.6-1.0 mM
8	sodium phosphate	natural abundance	45 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

4 3D CBCA(CO)NH

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.0

#	Name	Isotope labeling	Concentration
6	hJHBP	[U-13C; U-15N]	0.6-1.0 mM
7	JH III	natural abundance	0.6-1.0 mM
8	sodium phosphate	natural abundance	45 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

5 3D HNCA

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.0

#	Name	Isotope labeling	Concentration
6	hJHBP	[U-13C; U-15N]	0.6-1.0 mM
7	JH III	natural abundance	0.6-1.0 mM
8	sodium phosphate	natural abundance	45 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

6 3D HCABGCO

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.0

#	Name	Isotope labeling	Concentration
11	hJHBP	[U-13C; U-15N]	0.6-1.0 mM
12	JH III	natural abundance	0.6-1.0 mM
13	sodium phosphate	natural abundance	45 mM
14	D2O	natural abundance	100 %

7 3D HCCH-TOCSY

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.0

#	Name	Isotope labeling	Concentration
11	hJHBP	[U-13C; U-15N]	0.6-1.0 mM
12	JH III	natural abundance	0.6-1.0 mM
13	sodium phosphate	natural abundance	45 mM
14	D2O	natural abundance	100 %

8 3D 15N-separated HOHAHA-HSQC

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.0

#	Name	Isotope labeling	Concentration
1	hJHBP	[U-15N]	0.6-1.0 mM
2	JH III	natural abundance	0.6-1.0 mM
3	sodium phosphate	natural abundance	45 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

9 3D 15N-separated NOESY-HSQC

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 6.0

#	Name	Isotope labeling	Concentration
1	hJHBP	[U-15N]	0.6-1.0 mM
2	JH III	natural abundance	0.6-1.0 mM
3	sodium phosphate	natural abundance	45 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

10 3D 13C/15N-separated NOESY-HSQC

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.0

#	Name	Isotope labeling	Concentration
11	hJHBP	[U-13C; U-15N]	0.6-1.0 mM
12	JH III	natural abundance	0.6-1.0 mM
13	sodium phosphate	natural abundance	45 mM
14	D2O	natural abundance	100 %

11 3D 13C-separated NOESY-HSQC

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.0

#	Name	Isotope labeling	Concentration
11	hJHBP	[U-13C; U-15N]	0.6-1.0 mM
12	JH III	natural abundance	0.6-1.0 mM
13	sodium phosphate	natural abundance	45 mM
14	D2O	natural abundance	100 %

12 3D 13C/13C-separated NOESY-HSQC

Instrument

Bruker DMX - 750 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 308 K, pH 6.0

#	Name	Isotope labeling	Concentration
11	hJHBP	[U-13C; U-15N]	0.6-1.0 mM
12	JH III	natural abundance	0.6-1.0 mM
13	sodium phosphate	natural abundance	45 mM
14	D2O	natural abundance	100 %

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr16021_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)
1:11:CYS:SG	1:18:CYS:SG	oxidized, CA 51.792, CB 42.786 ppm	oxidized, CA 59.964, CB 37.519 ppm	n/a
1:153:CYS:SG	1:196:CYS:SG	oxidized, CA 52.662, CB 40.786 ppm	oxidized, CA 57.588, CB 37.131 ppm	n/a

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

None

Non-standard residues

None

Content subtype: bmr16021_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	2891		100.0 (chain: 1, length: 227)
1	Chemical shift references	chemical_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: 1, Chain length: 227, Sequence coverage: 100.0%

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

-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200
GDIVIELTEQSKSFTGLYTADTNVIGAVRYGYNLKNDDNGVQHFEVQPETFTCESIGEPKITLSSDLSSALEKDSGNNSLEPDMEPLKTLRQAAICKIAE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GDIVIELTEQSKSFTGLYTADTNVIGAVRYGYNLKNDDNGVQHFEVQPETFTCESIGEPKITLSSDLSSALEKDSGNNSLEPDMEPLKTLRQAAICKIAE

-------210-------220-------
ACYISVVHNIRASAKILPASSFFENLN
|||||||||||||||||||||||||||
ACYISVVHNIRASAKILPASSFFENLN

Total number of assignments
- ¹H chemical shifts: 1601
- ¹³C chemical shifts: 1048
- ¹⁵N chemical shifts: 242

Completeness of assignments

Entity_assemble_ID: 1

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
3	ASP	CG	177.807
5	ASP	CG	179.932
15	ASP	CG	181.092
17	GLN	CD	180.151
24	GLU	CD	183.349
25	GLN	CD	179.584
28	GLU	CD	182.932
36	GLN	CD	180.217
38	ASP	CG	181.689
43	ASP	CG	180.321
51	ASP	CG	178.886
57	ASP	CG	177.767
66	ASN	CG	178.397
68	ASN	CG	176.226
74	ASN	CG	177.07
75	GLN	CD	178.525
76	GLN	CD	180.512
79	ASP	CG	178.599
81	GLN	CD	179.859
83	ASP	CG	180.499
96	ASP	CG	180.367
102	ASP	CG	175.97
106	GLU	CD	182.912
109	GLU	CD	183.138
110	GLN	CD	179.473
121	ASP	CG	180.899
123	ASN	CG	176.592
133	ASN	CG	175.98
136	ASN	CG	175.414
137	ASP	CG	179.673
138	ASP	CG	179.813
139	ASN	CG	177.327
142	GLN	CD	179.111
145	GLU	CD	183.039
147	GLN	CD	179.175
149	GLU	CD	182.724
154	GLU	CD	181.774
158	GLU	CD	184.276
166	ASP	CG	179.508
172	GLU	CD	182.272
174	ASP	CG	179.153
177	ASN	CG	176.916
178	ASN	CG	177.142
181	GLU	CD	182.932
183	ASP	CG	180.559
185	GLU	CD	181.699
192	GLN	CD	179.752
200	GLU	CD	184.276
224	GLU	CD	182.15
225	ASN	CG	178.132
227	ASN	CG	178.159

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1341	1313	97.9
¹³C chemical shifts	1014	997	98.3
¹⁵N chemical shifts	244	242	99.2

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	457	455	99.6
¹³C chemical shifts	454	453	99.8
¹⁵N chemical shifts	217	215	99.1

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	884	858	97.1
¹³C chemical shifts	560	544	97.1
¹⁵N chemical shifts	27	27	100.0

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	144	144	100.0
¹³C chemical shifts	144	144	100.0

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	72	64	88.9
¹³C chemical shifts	71	63	88.7
¹⁵N chemical shifts	1	1	100.0

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

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Found 1 Document (0.515 seconds)

BMRB: 16021

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. hJHBP, : 1 : 3 : 3 entities Detail

Experiments performed 12 experiments Detail

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Chemical shift validation 3 contents Detail