BMRBj - BMREntryMaster

Found 1 Document (0.78 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

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.78 seconds)

BMRB: 30550

Sample #1

Sample #2

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

Experiments performed 18 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail