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Found 1 Document (0.652 seconds)

BMRB: 30445

6CWS

The NMR solution structure of CCL28

Authors

Thomas, M.A., Peterson, F.C., Volkman, B.F.

Assembly

C-C motif chemokine 28

Entity

1. C-C motif chemokine 28 (polymer), 108 monomers, 12361.15 Da Detail

SEAILPIASS CCTEVSHHIS RRLLERVNMC RIQRADGDCD LAAVILHVKR RRICVSPHNH TVKQWMKVQA AKKNGKGNVC HRKKHHGKRN SNRAHQGKHE TYGHKTPY

Formula weight

12361.15 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 91.2 %, Completeness (bb): 95.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	91.2 % (1151 of 1262)	90.0 % (600 of 667)	91.6 % (439 of 479)	96.6 % (112 of 116)
Backbone	95.5 % (613 of 642)	94.1 % (206 of 219)	95.9 % (305 of 318)	97.1 % (102 of 105)
Sidechain	88.1 % (636 of 722)	87.9 % (394 of 448)	88.2 % (232 of 263)	90.9 % (10 of 11)
Aromatic	55.6 % (40 of 72)	61.1 % (22 of 36)	48.6 % (17 of 35)	100.0 % (1 of 1)
Methyl	94.0 % (94 of 100)	92.0 % (46 of 50)	96.0 % (48 of 50)

1. entity 1

SEAILPIASS CCTEVSHHIS RRLLERVNMC RIQRADGDCD LAAVILHVKR RRICVSPHNH TVKQWMKVQA AKKNGKGNVC HRKKHHGKRN SNRAHQGKHE TYGHKTPY

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2, Details 0.7 mM [U-99% 13C; U-99% 15N] CCL28, 25 mM [U-99% 2H] MES, 0.02 % sodium azide, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	CCL28	[U-99% 13C; U-99% 15N]	0.7 mM
2	MES	[U-99% 2H]	25 mM
3	sodium azide	natural abundance	0.02 %

LACS Plot; CA

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

Referencing offset: -0.45 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: -0.45 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: 0.07 ppm, Outliers: 2 Detail

LACS Plot; CO

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

Referencing offset: -0.03 ppm, Outliers: 2 Detail

Release date

2018-04-08

Citation

The Solution Structure of CCL28 Reveals Structural Lability that Does Not Constrain Antifungal Activity
Thomas, M.A., He, J., Peterson, F.C., Suppler, A.R., Volkman, B.F.
J. Mol. Biol. (2018), 430, 3266-3282, PubMed 29913161 , DOI 10.1016/j.jmb.2018.06.001 , Abstract

Related entities 1. C-C motif chemokine 28, : 1 : 2 : 7 entities Detail

Interaction partners 1. C-C motif chemokine 28, : 24 interactors Detail

More details for 24 interactors identified by 5 citations

Experiments performed 3 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30445_6cws.nef
Input source #2: Coordindates	6cws.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:11:CYS:SG	A:39:CYS:SG	oxidized, CA 55.463, CB 40.573 ppm	oxidized, CA 52.511, CB 39.925 ppm	2.009
A:12:CYS:SG	A:54:CYS:SG	oxidized, CA 57.644, CB 42.226 ppm	oxidized, CA 55.093, CB 46.227 ppm	2.028
A:30:CYS:SG	A:80:CYS:SG	oxidized, CA 54.491, CB 49.309 ppm	oxidized, CA 54.486, CB 43.809 ppm	2.039

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
SEAILPIASSCCTEVSHHISRRLLERVNMCRIQRADGDCDLAAVILHVKRRRICVSPHNHTVKQWMKVQAAKKNGKGNVCHRKKHHGKRNSNRAHQGKHE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SEAILPIASSCCTEVSHHISRRLLERVNMCRIQRADGDCDLAAVILHVKRRRICVSPHNHTVKQWMKVQAAKKNGKGNVCHRKKHHGKRNSNRAHQGKHE

--------
TYGHKTPY
||||||||
TYGHKTPY

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	108	0	0	100.0

Content subtype: combined_30445_6cws.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_chemical_shifts_1	Warning	1152		99.1 (chain: A, length: 108)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	1961 (1)	noe	88.0 (chain: A, length: 108)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	9 (1)	undefined	5.6 (chain: A, length: 108)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_4	OK	105 (105)	.	61.1 (chain: A, length: 108)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 108, Sequence coverage: 99.1%
- Total number of assignments
  - ¹³C chemical shifts: 434
  - ¹H chemical shifts: 607
  - ¹⁵N chemical shifts: 111
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	479	434	90.6
¹H chemical shifts	667	607	91.0
¹⁵N chemical shifts	127	111	87.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	216	205	94.9
¹H chemical shifts	219	209	95.4
¹⁵N chemical shifts	105	101	96.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	263	229	87.1
¹H chemical shifts	448	398	88.8
¹⁵N chemical shifts	22	10	45.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	52	47	90.4
¹H chemical shifts	52	47	90.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	35	17	48.6
¹H chemical shifts	36	22	61.1
¹⁵N chemical shifts	1	1	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 108, Sequence coverage: 88.0%
- Total number of restraints: 1961
- Weight of restraints: 1.0 (1961)
- Potential type of restraints: upper-bound-parabolic (1961)
- Range of distance target values: 2.4, 5.5 (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: DYANA/DIANA_distance_constraints_3
  - Status: Warning
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 108, Sequence coverage: 5.6%
  - Total number of restraints: 9
  - Weight of restraints: 1.0 (9)
  - Potential type of restraints: upper-bound-parabolic (9)
  - Range of distance target values: 2.1, 3.1 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 108, Sequence coverage: 61.1%
- Total number of restraints: 105
- Total number of restraints per polymer type: 105
- Weight of restraints: 1.0 (105)
- Potential type of restraints: square-well-parabolic (105)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Antifungal activity, CCL28, CYTOKINE, Chemokine

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Found 1 Document (0.652 seconds)

BMRB: 30445

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. C-C motif chemokine 28, : 1 : 2 : 7 entities Detail

Interaction partners 1. C-C motif chemokine 28, : 24 interactors Detail

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail