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BMRB: 15000

2JM0

Solution structure of chicken villin headpiece subdomain containing a fluorinated side chain in the core

Authors

Cornilescu, C.C., Cornilescu, G., Hadley, E.B., Gellman, S.H., Markley, J.L.

Assembly

F5-Phe-cVHP

Entity

1. F5-Phe-cVHP (polymer, Thiol state: all free), 35 monomers, 5336.034 Da Detail

LSDEDFRAVX GMTRSAFANL PLWRQQNLRR ERGLF

Formula weight

5336.034 Da

Source organism

Exptl. method

Refine. method

torsion angle dynamics, molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.3 %, Completeness: 72.8 %, Completeness (bb): 80.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	72.8 % (303 of 416)	85.9 % (189 of 220)	51.3 % (81 of 158)	86.8 % (33 of 38)
Backbone	80.7 % (163 of 202)	97.1 % (67 of 69)	64.0 % (64 of 100)	97.0 % (32 of 33)
Sidechain	66.7 % (164 of 246)	80.8 % (122 of 151)	45.6 % (41 of 90)	20.0 % (1 of 5)
Aromatic	38.1 % (16 of 42)	71.4 % (15 of 21)	0.0 % (0 of 20)	100.0 % (1 of 1)
Methyl	62.5 % (20 of 32)	87.5 % (14 of 16)	37.5 % (6 of 16)

1. F5-Phe-cVHP

LSDEDFRAVX GMTRSAFANL PLWRQQNLRR ERGLF

Show sample condition

Sample #1

Pressure 1 atm, Temperature 298 (±0.2) K, pH 5.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	F5-Phe-cVHP	natural abundance		4 mM

Sample #2

Pressure 1 atm, Temperature 298 (±0.2) K, pH 5.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
2	F5-Phe-cVHP	[15N]-Ala, Phe, Leu		2 mM

Protein Blocks Logo

Calculated from 20 models in PDB: 2JM0, Strand ID: A Detail

Release date

2006-09-06

Citation

Solution structure of a small protein containing a fluorinated side chain in the core
Cornilescu, G., Hadley, E.B., Woll, M.G., Markley, J.L., Gellman, S.H., Cornilescu, C.C.
Protein Sci. (2007), 16, 14-19, PubMed 17123960 , DOI 10.1110/ps.062557707 , Abstract

Related entities 1. F5-Phe-cVHP, : 1 : 144 entities Detail

Interaction partners 1. F5-Phe-cVHP, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 500 MHz QNP room temperature probe

Sample

State isotropic, Pressure 1 atm, Temperature 298 (±0.2) K, pH 5.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	F5-Phe-cVHP	natural abundance		4 mM

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz cryogenic probe

Sample

State isotropic, Pressure 1 atm, Temperature 298 (±0.2) K, pH 5.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	F5-Phe-cVHP	natural abundance		4 mM

3 2D COSY

Instrument

Varian INOVA - 600 MHz cryogenic probe

Sample

State isotropic, Pressure 1 atm, Temperature 298 (±0.2) K, pH 5.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	F5-Phe-cVHP	natural abundance		4 mM

4 2D TOCSY

Instrument

Bruker Avance - 500 MHz cryogenic probe

Sample

State isotropic, Pressure 1 atm, Temperature 298 (±0.2) K, pH 5.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	F5-Phe-cVHP	natural abundance		4 mM

5 2D NOESY

Instrument

Bruker Avance - 500 MHz cryogenic probe

Sample

State isotropic, Pressure 1 atm, Temperature 298 (±0.2) K, pH 5.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	F5-Phe-cVHP	natural abundance		4 mM

6 2D 1H-15N HSQC

Instrument

Bruker Avance - 500 MHz cryogenic probe

Sample

State isotropic, Pressure 1 atm, Temperature 298 (±0.2) K, pH 5.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
2	F5-Phe-cVHP	[15N]-Ala, Phe, Leu		2 mM

7 2D HNCO

Instrument

Bruker Avance - 500 MHz cryogenic probe

Sample

State isotropic, Pressure 1 atm, Temperature 298 (±0.2) K, pH 5.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
2	F5-Phe-cVHP	[15N]-Ala, Phe, Leu		2 mM

8 2D HNCACB

Instrument

Varian INOVA - 800 MHz cryogenic probe

Sample

State isotropic, Pressure 1 atm, Temperature 298 (±0.2) K, pH 5.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
2	F5-Phe-cVHP	[15N]-Ala, Phe, Leu		2 mM

9 2D HNHA

Instrument

Varian INOVA - 800 MHz cryogenic probe

Sample

State isotropic, Pressure 1 atm, Temperature 298 (±0.2) K, pH 5.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
2	F5-Phe-cVHP	[15N]-Ala, Phe, Leu		2 mM

10 2D HNHB

Instrument

Varian INOVA - 800 MHz cryogenic probe

Sample

State isotropic, Pressure 1 atm, Temperature 298 (±0.2) K, pH 5.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
2	F5-Phe-cVHP	[15N]-Ala, Phe, Leu		2 mM

11 19F-HOESY

Instrument

Bruker Avance - 500 MHz QNP room temperature probe

Sample

State isotropic, Pressure 1 atm, Temperature 298 (±0.2) K, pH 5.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	F5-Phe-cVHP	natural abundance		4 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15000_2jm0.nef
Input source #2: Coordindates	2jm0.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	True (see coodinates for details)
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Error

Disulfide bonds

None

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

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:9:VAL:C	1:10:PF5:N	unknown	unknown	n/a
1:10:PF5:C	1:11:GLY:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	10	PF5	2,3,4,5,6-PENTAFLUORO-L-PHENYLALANINE	Assigned chemical shifts, Coordinates

Sequence alignments

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

--------10--------20--------30-----
LSDEDFRAVXGMTRSAFANLPLWRQQNLRRERGLF
|||||||||||||||||||||||||||||||||||
LSDEDFRAVXGMTRSAFANLPLWRQQNLRRERGLF

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	35	0	0	100.0

Content subtype: combined_15000_2jm0.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	310		97.1 (chain: A, length: 35)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1391 (1)	noe	94.3 (chain: A, length: 35)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	12 (1)	hbond	34.3 (chain: A, length: 35)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	Error	89 (89)	.	97.1 (chain: A, length: 35)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 35, Sequence coverage: 97.1%
- Total number of assignments
  - ¹H chemical shifts: 193
  - ¹³C chemical shifts: 77
  - ¹⁵N chemical shifts: 40
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: A

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 35, Sequence coverage: 94.3%
- Total number of restraints: 1318
- Weight of restraints: 1.0 (1318)
- Potential type of restraints: square-well-parabolic (1318)
- Range of distance target values: 1.9, 4.7 (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: 35, Sequence coverage: 34.3%
  - Total number of restraints: 12
  - Weight of restraints: 1.0 (12)
  - Potential type of restraints: square-well-parabolic (12)
  - Range of distance target values: 2.0, 3.0 (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_3
- Status: Error
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 35, Sequence coverage: 97.1%
- Total number of restraints: 89
- Total number of restraints per polymer type: 89
- Weight of restraints: 1.0 (89)
- Potential type of restraints: square-well-parabolic (89)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords VHP, chicken villin headpiece, fluorinated Phe