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BMRB: 17561

2LBH

Solution Structure of the Dimeric Form of a Unliganded Bovine Neurophysin, Minimized Average Structure

Authors

Lee, H., Naik, M., Nguyen, T., Bracken, C., Breslow, E.

Assembly

Unliganded Bovine Neurophysin

Entity

1. Unliganded Bovine Neurophysin (polymer), 92 monomers, 9288.415 × 2 Da Detail

AVLDLDVRTC LPCGPGGKGR CFGPSICCGD ELGCFVGTAE ALRCQEENYL PSPCQSGQKP CGSGGRCAAA GICCSPDGCH EDPACDPEAA FS

Total weight

18576.83 Da

Max. entity weight

9288.415 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 93.5 %, Completeness: 52.3 %, Completeness (bb): 58.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	52.3 % (482 of 921)	67.4 % (322 of 478)	22.8 % (81 of 356)	90.8 % (79 of 87)
Backbone	58.6 % (313 of 534)	89.4 % (169 of 189)	25.2 % (66 of 262)	94.0 % (78 of 83)
Sidechain	38.1 % (177 of 465)	52.9 % (153 of 289)	13.4 % (23 of 172)	25.0 % (1 of 4)
Aromatic	2.4 % (1 of 42)	4.8 % (1 of 21)	0.0 % (0 of 21)
Methyl	48.5 % (32 of 66)	72.7 % (24 of 33)	24.2 % (8 of 33)

1. Bovine Neurophysin

AVLDLDVRTC LPCGPGGKGR CFGPSICCGD ELGCFVGTAE ALRCQEENYL PSPCQSGQKP CGSGGRCAAA GICCSPDGCH EDPACDPEAA FS

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 2.7, Details 1 mM BNP1 of bovine neurophysin I

#	Name	Isotope labeling	Type	Concentration
1	Bovine Neurophysin	[U-100% 15N]		1 mM

Protein Blocks Logo

Calculated from 21 models in PDB: 2LBH, Strand ID: A, B Detail

Release date

2012-04-02

Citation

Structural Basis of the Dimerization-Induced Increase in Neurophysin-Hormone Affinity: Interplay of Inter-Domain and Inter-Subunit Interactions
Lee, H., Naik, M., Bracken, C., Breslow, E.
Not known

Related entities 1. Unliganded Bovine Neurophysin, : 1 : 1 : 6 : 52 entities Detail

Interaction partners 1. Unliganded Bovine Neurophysin, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 2.7, Details 1 mM BNP1 of bovine neurophysin I

#	Name	Isotope labeling	Type	Concentration
1	Bovine Neurophysin	[U-100% 15N]		1 mM

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 2.7, Details 1 mM BNP1 of bovine neurophysin I

#	Name	Isotope labeling	Type	Concentration
1	Bovine Neurophysin	[U-100% 15N]		1 mM

3 3D HNCA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 2.7, Details 1 mM BNP1 of bovine neurophysin I

#	Name	Isotope labeling	Type	Concentration
1	Bovine Neurophysin	[U-100% 15N]		1 mM

4 3D HN(CO)CA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 2.7, Details 1 mM BNP1 of bovine neurophysin I

#	Name	Isotope labeling	Type	Concentration
1	Bovine Neurophysin	[U-100% 15N]		1 mM

5 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 2.7, Details 1 mM BNP1 of bovine neurophysin I

#	Name	Isotope labeling	Type	Concentration
1	Bovine Neurophysin	[U-100% 15N]		1 mM

6 3D HNHA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 2.7, Details 1 mM BNP1 of bovine neurophysin I

#	Name	Isotope labeling	Type	Concentration
1	Bovine Neurophysin	[U-100% 15N]		1 mM

7 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 2.7, Details 1 mM BNP1 of bovine neurophysin I

#	Name	Isotope labeling	Type	Concentration
1	Bovine Neurophysin	[U-100% 15N]		1 mM

8 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 2.7, Details 1 mM BNP1 of bovine neurophysin I

#	Name	Isotope labeling	Type	Concentration
1	Bovine Neurophysin	[U-100% 15N]		1 mM

9 3D 1H-13C NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 2.7, Details 1 mM BNP1 of bovine neurophysin I

#	Name	Isotope labeling	Type	Concentration
1	Bovine Neurophysin	[U-100% 15N]		1 mM

10 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 308 K, pH 2.7, Details 1 mM BNP1 of bovine neurophysin I

#	Name	Isotope labeling	Type	Concentration
1	Bovine Neurophysin	[U-100% 15N]		1 mM

11 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 314 K, pH 2.7, Details 1 mM BNP1 of bovine neurophysin I

#	Name	Isotope labeling	Type	Concentration
1	Bovine Neurophysin	[U-100% 15N]		1 mM

12 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 2.7, Details 1 mM BNP1 of bovine neurophysin I

#	Name	Isotope labeling	Type	Concentration
1	Bovine Neurophysin	[U-100% 15N]		1 mM

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_17561_2lbh.nef
Input source #2: Coordindates	2lbh.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:10:CYS:SG	A:54:CYS:SG	unknown	unknown, CA 55.74 ppm	2.036
A:13:CYS:SG	A:27:CYS:SG	unknown, CA 54.53 ppm	unknown, CA 54.156 ppm	2.034
A:21:CYS:SG	A:44:CYS:SG	unknown, CA 56.183 ppm	unknown, CA 53.835 ppm	2.031
A:28:CYS:SG	A:34:CYS:SG	unknown, CA 55.39 ppm	unknown, CA 55.713 ppm	2.033
A:61:CYS:SG	A:73:CYS:SG	unknown	unknown, CA 54.156 ppm	2.033
A:67:CYS:SG	A:85:CYS:SG	unknown, CA 54.094 ppm	unknown, CA 51.59 ppm	2.032
A:74:CYS:SG	A:79:CYS:SG	unknown, CA 56.3 ppm	unknown	2.028
B:110:CYS:SG	B:154:CYS:SG	unknown	unknown	2.029
B:113:CYS:SG	B:127:CYS:SG	unknown	unknown	2.038
B:121:CYS:SG	B:144:CYS:SG	unknown	unknown	2.033
B:128:CYS:SG	B:134:CYS:SG	unknown	unknown	2.037
B:161:CYS:SG	B:173:CYS:SG	unknown	unknown	2.033
B:167:CYS:SG	B:185:CYS:SG	unknown	unknown	2.033
B:174:CYS:SG	B:179:CYS:SG	unknown	unknown	2.027

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

None

Non-standard residues

None

Sequence alignments

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

--------10--------20--------30--------40--------50--------60--------70--------80--------90--
AVLDLDVRTCLPCGPGGKGRCFGPSICCGDELGCFVGTAEALRCQEENYLPSPCQSGQKPCGSGGRCAAAGICCSPDGCHEDPACDPEAAFS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
AVLDLDVRTCLPCGPGGKGRCFGPSICCGDELGCFVGTAEALRCQEENYLPSPCQSGQKPCGSGGRCAAAGICCSPDGCHEDPACDPEAAFS

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

-------110-------120-------130-------140-------150-------160-------170-------180-------190--
AVLDLDVRTCLPCGPGGKGRCFGPSICCGDELGCFVGTAEALRCQEENYLPSPCQSGQKPCGSGGRCAAAGICCSPDGCHEDPACDPEAAFS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
AVLDLDVRTCLPCGPGGKGRCFGPSICCGDELGCFVGTAEALRCQEENYLPSPCQSGQKPCGSGGRCAAAGICCSPDGCHEDPACDPEAAFS
--------10--------20--------30--------40--------50--------60--------70--------80--------90--

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	92	0	0	100.0
B	B	92	0	0	100.0

Content subtype: combined_17561_2lbh.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	14		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	429		92.4 (chain: A, length: 92)
1	Distance restraints	CNS/XPLOR_distance_constraints_5	Warning	2084 (1)	noe	95.7 (chain: A, length: 92), 95.7 (chain: B, length: 92)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	115 (1)	hbond	44.6 (chain: A, length: 92), 44.6 (chain: B, length: 92)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	243 (243)	.	93.5 (chain: A, length: 92), 93.5 (chain: B, length: 92)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_4	OK	80 (80)	.	41.3 (chain: A, length: 92), 41.3 (chain: B, length: 92)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 92, Sequence coverage: 92.4%
- Total number of assignments
  - ¹H chemical shifts: 309
  - ¹⁵N chemical shifts: 77
  - ¹³C chemical shifts: 43
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_5
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 92, Sequence coverage: 95.7%
  - Entity_assembly_ID: B, Chain length: 92, Sequence coverage: 95.7%
- Total number of restraints: 2084
- Weight of restraints: 1.0 (2084)
- Potential type of restraints: square-well-parabolic (2084)
- Range of distance target values: 1.4, 5.1 (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_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 92, Sequence coverage: 44.6%
    - Entity_assembly_ID: B, Chain length: 92, Sequence coverage: 44.6%
  - Total number of restraints: 115
  - Weight of restraints: 1.0 (115)
  - Potential type of restraints: square-well-parabolic (115)
  - Range of distance target values: 1.9, 2.9 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 92, Sequence coverage: 93.5%
  - Entity_assembly_ID: B, Chain length: 92, Sequence coverage: 93.5%
- Total number of restraints: 243
- Total number of restraints per polymer type: 243
- Weight of restraints: 1.0 (243)
- Potential type of restraints: square-well-parabolic (243)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 92, Sequence coverage: 41.3%
  - Entity_assembly_ID: B, Chain length: 92, Sequence coverage: 41.3%
- Total number of restraints: 80
- Potential type of restraints: undefined (80)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue

Keywords neurophysin