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BMRB: 25666

2N4E

Solution NMR Structure of DE NOVO DESIGNED PROTEIN Top7NNSTYCC, Northeast Structural Genomics Consortium (NESG) Target OR34

Authors

Liu, G., Chan, K., Basanta, B., Xiao, R., Janjua, H., Kogan, S., Maglaqui, M., Ciccosanti, C., Acton, T.B., Kornhaber, G., Everett, J.K., Baker, D., Montelione, G.T.

Assembly

or34

Entity

1. or34 (polymer, Thiol state: all disulfide bound), 106 monomers, 12126.35 Da Detail

MHHHHHHRSG DIQVQNNNTC NGKTFDYTYT VTTESELQKV LNELKDYIKK QGCKRSRTSI TARTKKEAEK FAAILIKVYA ELGYNDINVT WDGDTVTVEG QLEGVD

Formula weight

12126.35 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS20:SG	1:CYS53:SG

Exptl. method

Refine. method

distance geometry, simulated annealing, molecular dynamics, null

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 89.6 %, Completeness: 73.4 %, Completeness (bb): 67.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	73.4 % (903 of 1231)	77.9 % (496 of 637)	66.7 % (317 of 475)	75.6 % (90 of 119)
Backbone	67.6 % (430 of 636)	75.3 % (165 of 219)	60.1 % (187 of 311)	73.6 % (78 of 106)
Sidechain	80.4 % (558 of 694)	79.2 % (331 of 418)	81.7 % (215 of 263)	92.3 % (12 of 13)
Aromatic	47.9 % (46 of 96)	52.1 % (25 of 48)	42.6 % (20 of 47)	100.0 % (1 of 1)
Methyl	98.2 % (112 of 114)	96.5 % (55 of 57)	100.0 % (57 of 57)

1. OR34

MHHHHHHRSG DIQVQNNNTC NGKTFDYTYT VTTESELQKV LNELKDYIKK QGCKRSRTSI TARTKKEAEK FAAILIKVYA ELGYNDINVT WDGDTVTVEG QLEGVD

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.369 mM or34.018, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	or34.018	[U-100% 13C; U-100% 15N]		0.369 mM
2	DTT	natural abundance		5 mM
3	NaCl	natural abundance		100 mM
4	Tris-HCl pH 7.5	natural abundance		10 mM
5	NaN3	natural abundance		0.02 %
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: -0.26 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.26 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.22 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2N4E, Strand ID: A Detail

Release date

2015-12-06

Related entities 1. or34, : 1 : 1 : 10 entities Detail

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.369 mM or34.018, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	or34.018	[U-100% 13C; U-100% 15N]		0.369 mM
2	DTT	natural abundance		5 mM
3	NaCl	natural abundance		100 mM
4	Tris-HCl pH 7.5	natural abundance		10 mM
5	NaN3	natural abundance		0.02 %
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.369 mM or34.018, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	or34.018	[U-100% 13C; U-100% 15N]		0.369 mM
2	DTT	natural abundance		5 mM
3	NaCl	natural abundance		100 mM
4	Tris-HCl pH 7.5	natural abundance		10 mM
5	NaN3	natural abundance		0.02 %
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

3 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.369 mM or34.018, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	or34.018	[U-100% 13C; U-100% 15N]		0.369 mM
2	DTT	natural abundance		5 mM
3	NaCl	natural abundance		100 mM
4	Tris-HCl pH 7.5	natural abundance		10 mM
5	NaN3	natural abundance		0.02 %
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

4 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.369 mM or34.018, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	or34.018	[U-100% 13C; U-100% 15N]		0.369 mM
2	DTT	natural abundance		5 mM
3	NaCl	natural abundance		100 mM
4	Tris-HCl pH 7.5	natural abundance		10 mM
5	NaN3	natural abundance		0.02 %
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

5 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.369 mM or34.018, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	or34.018	[U-100% 13C; U-100% 15N]		0.369 mM
2	DTT	natural abundance		5 mM
3	NaCl	natural abundance		100 mM
4	Tris-HCl pH 7.5	natural abundance		10 mM
5	NaN3	natural abundance		0.02 %
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

6 3D 1H-13C arom NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.369 mM or34.018, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	or34.018	[U-100% 13C; U-100% 15N]		0.369 mM
2	DTT	natural abundance		5 mM
3	NaCl	natural abundance		100 mM
4	Tris-HCl pH 7.5	natural abundance		10 mM
5	NaN3	natural abundance		0.02 %
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

7 3D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.369 mM or34.018, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	or34.018	[U-100% 13C; U-100% 15N]		0.369 mM
2	DTT	natural abundance		5 mM
3	NaCl	natural abundance		100 mM
4	Tris-HCl pH 7.5	natural abundance		10 mM
5	NaN3	natural abundance		0.02 %
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

8 3D CCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.369 mM or34.018, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	or34.018	[U-100% 13C; U-100% 15N]		0.369 mM
2	DTT	natural abundance		5 mM
3	NaCl	natural abundance		100 mM
4	Tris-HCl pH 7.5	natural abundance		10 mM
5	NaN3	natural abundance		0.02 %
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25666_2n4e.nef
Input source #2: Coordindates	2n4e.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:20:CYS:SG	A:53:CYS:SG	unknown	unknown	2.058

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-------100
MHHHHHHRSGDIQVQNNNTCNGKTFDYTYTVTTESELQKVLNELKDYIKKQGCKRSRTSITARTKKEAEKFAAILIKVYAELGYNDINVTWDGDTVTVEG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MHHHHHHRSGDIQVQNNNTCNGKTFDYTYTVTTESELQKVLNELKDYIKKQGCKRSRTSITARTKKEAEKFAAILIKVYAELGYNDINVTWDGDTVTVEG

------
QLEGVD
||||||
QLEGVD

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	106	0	0	100.0

Content subtype: combined_25666_2n4e.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	895		86.8 (chain: A, length: 106)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	3 (1)	undefined	1.9 (chain: A, length: 106)
2	Distance restraints	CNS/XPLOR_distance_constraints_5	OK	2635 (1)	noe	85.8 (chain: A, length: 106)
3	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	46 (1)	hbond	32.1 (chain: A, length: 106)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	134 (134)	.	77.4 (chain: A, length: 106)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 106, Sequence coverage: 86.8%
- Total number of assignments
  - ¹H chemical shifts: 509
  - ¹³C chemical shifts: 301
  - ¹⁵N chemical shifts: 85
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: Warning
- Experiment type: undefined
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 106, Sequence coverage: 1.9%
- Total number of restraints: 3
- Weight of restraints: 1.0 (3)
- Potential type of restraints: square-well-parabolic (3)
- Range of distance target values: 2.29, 3.4 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_5
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 106, Sequence coverage: 85.8%
  - Total number of restraints: 2626
  - Weight of restraints: 1.0 (2626)
  - Potential type of restraints: square-well-parabolic (2626)
  - Range of distance target values: 2.11, 4.35 (Å)
  - Histogram of distance target values
  - Histogram of discrepancy in distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_4
    - Status: OK
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 106, Sequence coverage: 32.1%
    - Total number of restraints: 46
    - Weight of restraints: 1.0 (46)
    - Potential type of restraints: square-well-parabolic (46)
    - Range of distance target values: 2.12, 3.2 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
    - 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: 106, Sequence coverage: 77.4%
- Total number of restraints: 134
- Total number of restraints per polymer type: 134
- Weight of restraints: 1.0 (134)
- Potential type of restraints: square-well-parabolic (134)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG), PSI-Biology, Protein NMR, Protein Structure Initiative, Structural Genomics, Target OR34