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Found 1 Document (0.496 seconds)

BMRB: 16387

2KL8

Solution NMR Structure of denovo designed ferrodoxin fold like protein, Northeast Structural Genomics Consortium Target Target OR15

Authors

Liu, G., Koga, N., Jiang, J., Xiao, R., Ciccosanti, C.Y., Locke, J.K., Everett, J., Nair, R.B., Acton, T., Rost, B.T., Baker, D., Montelione, G.

Assembly

OR15

Entity

1. OR15 (polymer, Thiol state: all free), 85 monomers, 10046.31 Da Detail

MEMDIRFRGD DLEAFEKALK EMIRQARKFA GTVTYTLDGN DLEIRITGVP EQVRKELAKE AERLAKEFNI TVTYTIRLEH HHHHH

Formula weight

10046.31 Da

Exptl. method

solution NMR

Refine. method

distance geometry, simulated annealing, molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.1 %, Completeness: 89.9 %, Completeness (bb): 91.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.9 % (919 of 1022)	91.0 % (486 of 534)	87.7 % (351 of 400)	93.2 % (82 of 88)
Backbone	91.3 % (464 of 508)	92.5 % (160 of 173)	90.0 % (226 of 251)	92.9 % (78 of 84)
Sidechain	89.2 % (531 of 595)	90.3 % (326 of 361)	87.4 % (201 of 230)	100.0 % (4 of 4)
Aromatic	55.0 % (44 of 80)	70.0 % (28 of 40)	40.0 % (16 of 40)
Methyl	100.0 % (96 of 96)	100.0 % (48 of 48)	100.0 % (48 of 48)

1. OR15

MEMDIRFRGD DLEAFEKALK EMIRQARKFA GTVTYTLDGN DLEIRITGVP EQVRKELAKE AERLAKEFNI TVTYTIRLEH HHHHH

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1.0 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	OR15	[U-100% 13C; U-100% 15N]		0.47 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.13 ppm, Outliers: 3 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.13 ppm, Outliers: 3 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.12 ppm, Outliers: 3 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.39 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2KL8, Strand ID: A Detail

Release date

2009-08-05

Citation

Principles for designing ideal protein structures
Koga, N., Tatsumi-Koga, R., Liu, G., Xiao, R., Acton, T.B., Montelione, G.T., Baker, D.
Nature (2012), 491, 222-227, PubMed 23135467 , DOI 10.1038/nature11600 , Abstract

Related entities 1. OR15, : 1 : 13 entities Detail

Experiments performed 9 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16387_2kl8.nef
Input source #2: Coordindates	2kl8.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	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

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-----
MEMDIRFRGDDLEAFEKALKEMIRQARKFAGTVTYTLDGNDLEIRITGVPEQVRKELAKEAERLAKEFNITVTYTIRLEHHHHHH
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MEMDIRFRGDDLEAFEKALKEMIRQARKFAGTVTYTLDGNDLEIRITGVPEQVRKELAKEAERLAKEFNITVTYTIRLEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	85	0	0	100.0

Content subtype: combined_16387_2kl8.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	928		94.1 (chain: A, length: 85)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1951 (1)	noe	92.9 (chain: A, length: 85)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	60 (1)	hbond	48.2 (chain: A, length: 85)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	128 (128)	.	88.2 (chain: A, length: 85)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 85, Sequence coverage: 94.1%
- Total number of assignments
  - ¹H chemical shifts: 495
  - ¹³C chemical shifts: 349
  - ¹⁵N chemical shifts: 84
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	534	495	92.7
¹³C chemical shifts	400	349	87.3
¹⁵N chemical shifts	96	84	87.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	173	162	93.6
¹³C chemical shifts	170	148	87.1
¹⁵N chemical shifts	84	78	92.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	361	333	92.2
¹³C chemical shifts	230	201	87.4
¹⁵N chemical shifts	12	6	50.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	51	51	100.0
¹³C chemical shifts	51	51	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	40	28	70.0
¹³C chemical shifts	40	16	40.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 85, Sequence coverage: 92.9%
- Total number of restraints: 1951
- Weight of restraints: 1.0 (1951)
- Potential type of restraints: square-well-parabolic (1951)
- Range of distance target values: 2.22, 4.64 (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: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 85, Sequence coverage: 48.2%
  - Total number of restraints: 60
  - Weight of restraints: 1.0 (60)
  - Potential type of restraints: square-well-parabolic (60)
  - Range of distance target values: 2.05, 2.62 (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_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 85, Sequence coverage: 88.2%
- Total number of restraints: 128
- Total number of restraints per polymer type: 128
- Weight of restraints: 1.0 (128)
- Potential type of restraints: square-well-parabolic (128)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG), Protein NMR, Protein Structure Initiative, PSI-2, Structural Genomics, Target OR15

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Found 1 Document (0.496 seconds)

BMRB: 16387

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. OR15, : 1 : 13 entities Detail

Experiments performed 9 experiments Detail

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NMR combined restraints 5 contents Detail