BMRBj - BMREntryMaster

Found 1 Document (0.738 seconds)

BMRB: 18210

2LOE

Structure of the Plasmodium 6-cysteine s48/45 Domain

Authors

Cai, M., Arredondo, S.A., Clore, M.G., Miller, L.H., Takayama, Y., Macdonald, N.J., Enderson, E.D., Aravind, L.

Assembly

Conotoxin analogue [D-Ala2]BuIIIB

Entity

1. Conotoxin analogue [D-Ala2]BuIIIB (polymer, Thiol state: all disulfide bound), 128 monomers, 14536.12 Da Detail

EKVKGCDFTT SESTIFSKGY SINEISNKSS NNQQDIVCTV KAHANDLIGF KCPSNYSVEP HDCFVSAFNL SGKNENLENK LKLTNIIMDH YNNTFYSRLP SLISDNWKFF CVCSKDNEKK LVFTVEAX

Formula weight

14536.12 Da

Entity Connection

disulfide 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS6:SG	1:CYS38:SG
2	disulfide	sing	1:CYS63:SG	1:CYS111:SG
3	disulfide	sing	1:CYS52:SG	1:CYS113:SG

Source organism

Plasmodium falciparum

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.2 %, Completeness: 91.3 %, Completeness (bb): 89.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	91.3 % (1369 of 1499)	89.2 % (694 of 778)	98.6 % (571 of 579)	73.2 % (104 of 142)
Backbone	89.8 % (679 of 756)	87.1 % (222 of 255)	98.1 % (370 of 377)	70.2 % (87 of 124)
Sidechain	93.8 % (812 of 866)	90.2 % (472 of 523)	99.4 % (323 of 325)	94.4 % (17 of 18)
Aromatic	100.0 % (146 of 146)	100.0 % (73 of 73)	100.0 % (72 of 72)	100.0 % (1 of 1)
Methyl	99.2 % (117 of 118)	98.3 % (58 of 59)	100.0 % (59 of 59)

1. entity

EKVKGCDFTT SESTIFSKGY SINEISNKSS NNQQDIVCTV KAHANDLIGF KCPSNYSVEP HDCFVSAFNL SGKNENLENK LKLTNIIMDH YNNTFYSRLP SLISDNWKFF CVCSKDNEKK LVFTVEAX

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 5.0

#	Name	Isotope labeling	Type	Concentration
1	Pf1 phage	[U-99% 13C; U-99% 15N]		0.4 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %

LACS Plot; CA

Referencing offset: -0.1 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: -0.1 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: -0.04 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.67 ppm, Outliers: 3 Detail

Protein Blocks Logo

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

Release date

2012-05-07

Citation

Structure of the Plasmodium 6-cysteine s48/45 domain
Arredondo, S.A., Cai, M., Takayama, Y., Macdonald, N.J., Anderson, D., Aravind, L., Clore, G., Miller, L.H.
Proc. Natl. Acad. Sci. U. S. A. (2012), 109, 6692-6697, PubMed 22493233 , DOI 10.1073/pnas.1204363109 , Abstract

Related entities 1. Conotoxin analogue [D-Ala2]BuIIIB, : 1 : 4 : 12 entities Detail

Experiments performed 10 experiments Detail

1 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 5.0

#	Name	Isotope labeling	Type	Concentration
1	Pf1 phage	[U-99% 13C; U-99% 15N]		0.4 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %

2 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 5.0

#	Name	Isotope labeling	Type	Concentration
1	Pf1 phage	[U-99% 13C; U-99% 15N]		0.4 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 5.0

#	Name	Isotope labeling	Type	Concentration
1	Pf1 phage	[U-99% 13C; U-99% 15N]		0.4 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %

4 3D HBHA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 5.0

#	Name	Isotope labeling	Type	Concentration
1	Pf1 phage	[U-99% 13C; U-99% 15N]		0.4 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %

5 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 5.0

#	Name	Isotope labeling	Type	Concentration
1	Pf1 phage	[U-99% 13C; U-99% 15N]		0.4 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %

6 3D 1H-15N NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 5.0

#	Name	Isotope labeling	Type	Concentration
1	Pf1 phage	[U-99% 13C; U-99% 15N]		0.4 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %

7 3D 1H-13C NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 5.0

#	Name	Isotope labeling	Type	Concentration
1	Pf1 phage	[U-99% 13C; U-99% 15N]		0.4 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %

8 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 5.0

#	Name	Isotope labeling	Type	Concentration
1	Pf1 phage	[U-99% 13C; U-99% 15N]		0.4 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %

9 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 5.0

#	Name	Isotope labeling	Type	Concentration
1	Pf1 phage	[U-99% 13C; U-99% 15N]		0.4 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %

10 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 308 K, pH 5.0

#	Name	Isotope labeling	Type	Concentration
1	Pf1 phage	[U-99% 13C; U-99% 15N]		0.4 mM
2	H2O	natural abundance		95 %
3	D2O	natural abundance		5 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18210_2loe.nef
Input source #2: Coordindates	2loe.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:6:CYS:SG	A:38:CYS:SG	oxidized, CA 54.85, CB 51.15 ppm	oxidized, CA 55.218, CB 49.957 ppm	2.021
A:52:CYS:SG	A:113:CYS:SG	oxidized, CA 52.191, CB 41.187 ppm	oxidized, CA 52.821, CB 43.946 ppm	2.023
A:63:CYS:SG	A:111:CYS:SG	oxidized, CA 59.504, CB 41.081 ppm	oxidized, CA 53.852, CB 47.83 ppm	2.022

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
EKVKGCDFTTSESTIFSKGYSINEISNKSSNNQQDIVCTVKAHANDLIGFKCPSNYSVEPHDCFVSAFNLSGKNENLENKLKLTNIIMDHYNNTFYSRLP
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
EKVKGCDFTTSESTIFSKGYSINEISNKSSNNQQDIVCTVKAHANDLIGFKCPSNYSVEPHDCFVSAFNLSGKNENLENKLKLTNIIMDHYNNTFYSRLP

-------110-------120-------
SLISDNWKFFCVCSKDNEKKLVFTVEA
|||||||||||||||||||||||||||
SLISDNWKFFCVCSKDNEKKLVFTVEA

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	127	0	0	100.0

Content subtype: combined_18210_2loe.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_chem_shift_list_1	Warning	1340		100.0 (chain: A, length: 127)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1652 (1)	noe	96.9 (chain: A, length: 127)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	686 (1)	noe	100.0 (chain: A, length: 127)
3	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	68 (1)	hbond	29.1 (chain: A, length: 127)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_5	OK	380 (380)	.	100.0 (chain: A, length: 127)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 127, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 671
  - ¹³C chemical shifts: 573
  - ¹⁵N chemical shifts: 96
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

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: 127, Sequence coverage: 96.9%
- Total number of restraints: 1625
- Weight of restraints: 1.0 (1625)
- Potential type of restraints: square-well-parabolic (1625)
- Range of distance target values: 2.25, 4.4 (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_3
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 127, Sequence coverage: 100.0%
  - Total number of restraints: 684
  - Weight of restraints: 1.0 (684)
  - Potential type of restraints: square-well-parabolic (684)
  - Range of distance target values: 2.35, 4.65 (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: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 127, Sequence coverage: 29.1%
    - Total number of restraints: 68
    - Weight of restraints: 1.0 (68)
    - Potential type of restraints: square-well-parabolic (68)
    - Range of distance target values: 1.9, 2.9 (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_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 127, Sequence coverage: 100.0%
- Total number of restraints: 380
- Total number of restraints per polymer type: 380
- Weight of restraints: 1.0 (380)
- Potential type of restraints: square-well-parabolic (380)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Malaria, pf12, p. falciparum, s48/14