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Found 1 Document (0.886 seconds)

BMRB: 30550

6NBN

Structure of Aedes aegypti OBP22 in the complex with arachidonic acid

Authors

Jones, D.N., Wang, J.

Assembly

AAEL005772-PA

Entity

1. AAEL005772-PA, entity 1 (polymer, Thiol state: all disulfide bound), 123 monomers, 14380.15 Da Detail

MEFTVSTTED LQRYRTECVS SLNIPADYVE KFKKWEFPED DTTMCYIKCV FNKMQLFDDT EGPLVDNLVH QLAHGRDAEE VRTEVLKCVD KNTDNNACHW AFRGFKCFQK NNLSLIKASI KKD

2. AAEL005772-PA, entity ACD (non-polymer), 304.467 Da

Total weight

14684.617 Da

Max. entity weight

14380.15 Da

Entity Connection

disulfide 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS18:SG	1:CYS49:SG
2	disulfide	sing	1:CYS45:SG	1:CYS98:SG
3	disulfide	sing	1:CYS88:SG	1:CYS107:SG

Source organism

Aedes aegypti

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 99.2 %, Completeness: 94.6 %, Completeness (bb): 97.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	94.6 % (1395 of 1474)	94.3 % (724 of 768)	94.2 % (539 of 572)	98.5 % (132 of 134)
Backbone	97.5 % (714 of 732)	97.2 % (239 of 246)	97.5 % (357 of 366)	98.3 % (118 of 120)
Sidechain	92.8 % (800 of 862)	92.9 % (485 of 522)	92.3 % (301 of 326)	100.0 % (14 of 14)
Aromatic	87.1 % (122 of 140)	95.7 % (67 of 70)	77.9 % (53 of 68)	100.0 % (2 of 2)
Methyl	100.0 % (118 of 118)	100.0 % (59 of 59)	100.0 % (59 of 59)

1. entity 1

MEFTVSTTED LQRYRTECVS SLNIPADYVE KFKKWEFPED DTTMCYIKCV FNKMQLFDDT EGPLVDNLVH QLAHGRDAEE VRTEVLKCVD KNTDNNACHW AFRGFKCFQK NNLSLIKASI KKD

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 820 (±10) mbar, Temperature 298 (±1) K, pH 6.5 (±0.1), Details 650 uM [U-13C; U-15N] OBP22, 650 uM ARACHIDONIC ACID, 20 mM sodium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	OBP22	[U-13C; U-15N]	650 (±15.0) uM
2	ARACHIDONIC ACID	natural abundance	650 (±30.0) uM
3	sodium phosphate	natural abundance	20 (±0.2) mM

Sample #2

Solvent system 99% D2O/1 % H2O, Pressure 820 (±10) mbar, Temperature 298 (±1) K, pH 6.5 (±0.1), Details 670 uM [U-95% 13C; U-98% 15N] Aedes aegypti odorant binding protein 22, 670 uM ARACHIDONIC ACID, 20 mM sodium phosphate, 99% D2O/1 % H2O

#	Name	Isotope labeling	Concentration
4	ARACHIDONIC ACID	natural abundance	670 (±30.0) uM
5	sodium phosphate	natural abundance	20 (±0.2) mM
6	Aedes aegypti odorant binding protein 22	[U-95% 13C; U-98% 15N]	670 (±15.0) uM

Protein Blocks Logo

Calculated from 30 models in PDB: 6NBN, Strand ID: A Detail

Release date

2018-12-11

Citation

Aedes aegypti Odorant Binding Protein 22 selectively binds fatty acids through a conformational change in its C-terminal tail
Wang, J., Murphy, E.J., Nix, J.C., Jones, D.
Sci. Rep. (2020), 10, 3300-3300, PubMed 32094450 , DOI 10.1038/s41598-020-60242-9 , Abstract

Related entities 1. AAEL005772-PA, entity 1, : 1 : 7 : 38 entities Detail

Experiments performed 18 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian DD2 - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 820 (±10) mbar, Temperature 298 (±1) K, pH 6.5 (±0.1), Details 650 uM [U-13C; U-15N] OBP22, 650 uM ARACHIDONIC ACID, 20 mM sodium phosphate, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	OBP22	[U-13C; U-15N]	650 (±15.0) uM
2	ARACHIDONIC ACID	natural abundance	650 (±30.0) uM
3	sodium phosphate	natural abundance	20 (±0.2) mM

2 2D 1H-13C HSQC aliphatic

Instrument

Varian DD2 - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	OBP22	[U-13C; U-15N]	650 (±15.0) uM
2	ARACHIDONIC ACID	natural abundance	650 (±30.0) uM
3	sodium phosphate	natural abundance	20 (±0.2) mM

3 2D 1H-13C HSQC aromatic

Instrument

Varian DD2 - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	OBP22	[U-13C; U-15N]	650 (±15.0) uM
2	ARACHIDONIC ACID	natural abundance	650 (±30.0) uM
3	sodium phosphate	natural abundance	20 (±0.2) mM

4 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	OBP22	[U-13C; U-15N]	650 (±15.0) uM
2	ARACHIDONIC ACID	natural abundance	650 (±30.0) uM
3	sodium phosphate	natural abundance	20 (±0.2) mM

5 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	OBP22	[U-13C; U-15N]	650 (±15.0) uM
2	ARACHIDONIC ACID	natural abundance	650 (±30.0) uM
3	sodium phosphate	natural abundance	20 (±0.2) mM

6 3D C(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	OBP22	[U-13C; U-15N]	650 (±15.0) uM
2	ARACHIDONIC ACID	natural abundance	650 (±30.0) uM
3	sodium phosphate	natural abundance	20 (±0.2) mM

7 3D 13C/15N- NOESY-HSQC

Instrument

Varian DD2 - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	OBP22	[U-13C; U-15N]	650 (±15.0) uM
2	ARACHIDONIC ACID	natural abundance	650 (±30.0) uM
3	sodium phosphate	natural abundance	20 (±0.2) mM

8 3D (HACA)CO(CA)NH

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	OBP22	[U-13C; U-15N]	650 (±15.0) uM
2	ARACHIDONIC ACID	natural abundance	650 (±30.0) uM
3	sodium phosphate	natural abundance	20 (±0.2) mM

9 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	OBP22	[U-13C; U-15N]	650 (±15.0) uM
2	ARACHIDONIC ACID	natural abundance	650 (±30.0) uM
3	sodium phosphate	natural abundance	20 (±0.2) mM

10 3D HBHA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	OBP22	[U-13C; U-15N]	650 (±15.0) uM
2	ARACHIDONIC ACID	natural abundance	650 (±30.0) uM
3	sodium phosphate	natural abundance	20 (±0.2) mM

11 2D 12C-filtered-1H-1H-NOESY

Instrument

Varian DD2 - 900 MHz

Sample

State isotropic, Solvent system 99% D2O/1 % H2O, Pressure 820 (±5) mbar, Temperature 298 (±1) K, pH 6.1 (±0.05), Details 670 uM [U-95% 13C; U-98% 15N] Aedes aegypti odorant binding protein 22, 670 uM ARACHIDONIC ACID, 20 mM sodium phosphate, 99% D2O/1 % H2O

#	Name	Isotope labeling	Concentration
4	ARACHIDONIC ACID	natural abundance	670 (±30.0) uM
5	sodium phosphate	natural abundance	20 (±0.2) mM
6	Aedes aegypti odorant binding protein 22	[U-95% 13C; U-98% 15N]	670 (±15.0) uM

12 3D 12C-filtered-13C/15N-editedNOESY-HSQC

Instrument

Varian DD2 - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
4	ARACHIDONIC ACID	natural abundance	670 (±30.0) uM
5	sodium phosphate	natural abundance	20 (±0.2) mM
6	Aedes aegypti odorant binding protein 22	[U-95% 13C; U-98% 15N]	670 (±15.0) uM

13 3D 13C/15N-NOESY-HSQC (AROMATIC)

Instrument

Varian DD2 - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	OBP22	[U-13C; U-15N]	650 (±15.0) uM
2	ARACHIDONIC ACID	natural abundance	650 (±30.0) uM
3	sodium phosphate	natural abundance	20 (±0.2) mM

14 3D HAHB

Instrument

Varian DD2 - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
4	ARACHIDONIC ACID	natural abundance	670 (±30.0) uM
5	sodium phosphate	natural abundance	20 (±0.2) mM
6	Aedes aegypti odorant binding protein 22	[U-95% 13C; U-98% 15N]	670 (±15.0) uM

15 2D 12C-filterd-1H-1H-TOCSY

Instrument

Varian DD2 - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
4	ARACHIDONIC ACID	natural abundance	670 (±30.0) uM
5	sodium phosphate	natural abundance	20 (±0.2) mM
6	Aedes aegypti odorant binding protein 22	[U-95% 13C; U-98% 15N]	670 (±15.0) uM

16 2D (HB)CB(CGCDCE)HE

Instrument

Varian DD2 - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
4	ARACHIDONIC ACID	natural abundance	670 (±30.0) uM
5	sodium phosphate	natural abundance	20 (±0.2) mM
6	Aedes aegypti odorant binding protein 22	[U-95% 13C; U-98% 15N]	670 (±15.0) uM

17 2D (HB)CB(CGCD)HD

Instrument

Varian DD2 - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
4	ARACHIDONIC ACID	natural abundance	670 (±30.0) uM
5	sodium phosphate	natural abundance	20 (±0.2) mM
6	Aedes aegypti odorant binding protein 22	[U-95% 13C; U-98% 15N]	670 (±15.0) uM

18 3D 1H-13C NOESY aromatic

Instrument

Varian DD2 - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
4	ARACHIDONIC ACID	natural abundance	670 (±30.0) uM
5	sodium phosphate	natural abundance	20 (±0.2) mM
6	Aedes aegypti odorant binding protein 22	[U-95% 13C; U-98% 15N]	670 (±15.0) uM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30550_6nbn.nef
Input source #2: Coordindates	6nbn.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	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:18:CYS:SG	A:49:CYS:SG	oxidized, CA 59.568, CB 41.522 ppm	oxidized, CA 60.365, CB 40.788 ppm	2.032
A:45:CYS:SG	A:98:CYS:SG	oxidized, CA 54.733, CB 37.011 ppm	oxidized, CA 60.136, CB 41.509 ppm	2.035
A:88:CYS:SG	A:107:CYS:SG	oxidized, CA 52.684, CB 40.339 ppm	oxidized, CA 59.427, CB 36.552 ppm	2.035

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

None

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	ACD	ARACHIDONIC ACID	Assigned chemical shifts, Distance restraints

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

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

-------110-------120---
AFRGFKCFQKNNLSLIKASIKKD
|||||||||||||||||||||||
AFRGFKCFQKNNLSLIKASIKKD

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	123	0	0	100.0

Content subtype: combined_30550_6nbn.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	3		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1435		99.2 (chain: A, length: 123), 100.0 (chain: B, length: 1)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	2293 (1)	noe	99.2 (chain: A, length: 123), 100.0 (chain: B, length: 1)
2	Distance restraints	CNS/XPLOR_distance_constraints_5	OK	42 (1)	hbond	47.2 (chain: A, length: 123)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	225 (225)	.	98.4 (chain: A, length: 123)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 123, Sequence coverage: 99.2%
  - Entity_assembly_ID: B, Chain length: 1, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 761
  - ¹³C chemical shifts: 537
  - ¹⁵N chemical shifts: 137
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- 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: A

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
43	THR	HG1	5.231
103	ARG	HH12	6.591
103	ARG	HH21	6.591
119	SER	HG	5.259

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	768	728	94.8
¹³C chemical shifts	572	537	93.9
¹⁵N chemical shifts	139	137	98.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	246	243	98.8
¹³C chemical shifts	246	237	96.3
¹⁵N chemical shifts	120	118	98.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	522	485	92.9
¹³C chemical shifts	326	300	92.0
¹⁵N chemical shifts	19	19	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	62	61	98.4
¹³C chemical shifts	62	61	98.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	70	67	95.7
¹³C chemical shifts	68	53	77.9
¹⁵N chemical shifts	2	2	100.0

Comp_index_ID	Comp_ID
1	ACD

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 123, Sequence coverage: 99.2%
  - Entity_assembly_ID: B, Chain length: 1, Sequence coverage: 100.0%
- Total number of restraints: 2282
- Weight of restraints: 1.0 (2282)
- Potential type of restraints: square-well-parabolic (2282)
- Range of distance target values: 1.54, 4.99 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_5
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 123, Sequence coverage: 47.2%
  - Total number of restraints: 42
  - Weight of restraints: 1.0 (42)
  - Potential type of restraints: square-well-parabolic (42)
  - Range of distance target values: 2.21, 2.46 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 123, Sequence coverage: 98.4%
- Total number of restraints: 225
- Total number of restraints per polymer type: 225
- Weight of restraints: 1.0 (225)
- Potential type of restraints: square-well-parabolic (225)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Odorant binding protein Chemo-sensory signaling Lipid binding, TRANSPORT PROTEIN

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Found 1 Document (0.886 seconds)

BMRB: 30550

Sample #1

Sample #2

Related entities 1. AAEL005772-PA, entity 1, : 1 : 7 : 38 entities Detail

Experiments performed 18 experiments Detail

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NMR combined restraints 5 contents Detail