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BMRB: 30525

6MM4

Solution NMR Structure of Engineered Cystine Knot Protein 2.5F

Authors

Cochran, F.V., Cochran, J.R.

Assembly

Engineered Cystine Knot Protein 2.5F

Entity

1. Engineered Cystine Knot Protein 2.5F (polymer, Thiol state: all disulfide bound), 33 monomers, 3297.681 Da Detail

GCPRPRGDNP PLTCSQDSDC LAGCVCGPNG FCG

Formula weight

3297.681 Da

Entity Connection

disulfide 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS2:SG	1:CYS24:SG
2	disulfide	sing	1:CYS14:SG	1:CYS26:SG
3	disulfide	sing	1:CYS20:SG	1:CYS32:SG

Source organism

synthetic construct

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 97.5 %, Completeness (bb): 96.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	97.5 % (315 of 323)	98.8 % (168 of 170)	95.1 % (116 of 122)	100.0 % (31 of 31)
Backbone	96.8 % (182 of 188)	100.0 % (67 of 67)	93.5 % (87 of 93)	100.0 % (28 of 28)
Sidechain	98.8 % (160 of 162)	98.1 % (101 of 103)	100.0 % (56 of 56)	100.0 % (3 of 3)
Aromatic	100.0 % (10 of 10)	100.0 % (5 of 5)	100.0 % (5 of 5)
Methyl	100.0 % (16 of 16)	100.0 % (8 of 8)	100.0 % (8 of 8)

1. entity 1

GCPRPRGDNP PLTCSQDSDC LAGCVCGPNG FCG

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 6.0, Details 400 uM [U-13C; U-15N] 2.5F, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	2.5F	[U-13C; U-15N]		400 uM

Protein Blocks Logo

Calculated from 20 models in PDB: 6MM4, Strand ID: A Detail

Release date

2018-10-17

Related entities 1. Engineered Cystine Knot Protein 2.5F, : 1 : 1 : 14 entities Detail

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian VNMRS - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 6.0, Details 400 uM [U-13C; U-15N] 2.5F, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	2.5F	[U-13C; U-15N]		400 uM

2 2D 1H-13C HSQC aliphatic

Instrument

Varian VNMRS - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 6.0, Details 400 uM [U-13C; U-15N] 2.5F, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	2.5F	[U-13C; U-15N]		400 uM

3 2D 1H-13C HSQC aromatic

Instrument

Varian VNMRS - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 6.0, Details 400 uM [U-13C; U-15N] 2.5F, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	2.5F	[U-13C; U-15N]		400 uM

4 3D C(CO)NH

Instrument

Varian VNMRS - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 6.0, Details 400 uM [U-13C; U-15N] 2.5F, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	2.5F	[U-13C; U-15N]		400 uM

5 3D HNCO

Instrument

Varian VNMRS - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 6.0, Details 400 uM [U-13C; U-15N] 2.5F, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	2.5F	[U-13C; U-15N]		400 uM

6 3D HNCACB

Instrument

Varian VNMRS - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 6.0, Details 400 uM [U-13C; U-15N] 2.5F, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	2.5F	[U-13C; U-15N]		400 uM

7 3D H(CCO)NH

Instrument

Varian VNMRS - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 6.0, Details 400 uM [U-13C; U-15N] 2.5F, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	2.5F	[U-13C; U-15N]		400 uM

8 3D 1H-15N NOESY

Instrument

Varian VNMRS - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 6.0, Details 400 uM [U-13C; U-15N] 2.5F, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	2.5F	[U-13C; U-15N]		400 uM

9 3D 1H-13C NOESY aliphatic

Instrument

Varian VNMRS - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 6.0, Details 400 uM [U-13C; U-15N] 2.5F, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	2.5F	[U-13C; U-15N]		400 uM

10 3D 1H-13C NOESY aromatic

Instrument

Varian VNMRS - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 6.0, Details 400 uM [U-13C; U-15N] 2.5F, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	2.5F	[U-13C; U-15N]		400 uM

11 GHNCO_LRA

Instrument

Varian VNS - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 6.0, Details 400 uM [U-13C; U-15N] 2.5F, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	2.5F	[U-13C; U-15N]		400 uM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr30525_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	OK

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:2:CYS:SG	1:24:CYS:SG	oxidized, CA 52.558, CB 41.086 ppm	oxidized, CA 55.092, CB 46.231 ppm	n/a
1:14:CYS:SG	1:26:CYS:SG	oxidized, CA 53.976, CB 47.736 ppm	oxidized, CA 55.262, CB 38.635 ppm	n/a
1:20:CYS:SG	1:32:CYS:SG	oxidized, CA 52.205, CB 40.173 ppm	oxidized, CA 55.572, CB 42.373 ppm	n/a

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

None

Non-standard residues

None

Content subtype: bmr30525_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	OK	329		100.0 (chain: 1, length: 33)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 33, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 183
  - ¹³C chemical shifts: 116
  - ¹⁵N chemical shifts: 30
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- Peptide bond of PRO
- 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

Keywords Cystine Knot, Knottin, Protein Binding, Protein Engineering