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Found 1 Document (0.847 seconds)

BMRB: 17890

2LIE

NMR structure of the lectin CCL2 (free)

Authors

Schubert, M., Walti, M.A., Egloff, P., Bleuler-Martinez, S., Aebi, M., Allain, F.F., Kunzler, M.

Assembly

CCL2 (free)

Entity

1. CCL2 (free) (polymer), 153 monomers, 16586.12 Da Detail

MGHHHHHHHH SGDSPAVTLS AGNYIIYNRV LSPRGEKLAL TYPGRQRTPV TVSPLDGSSE QAWILRSYDS NSNTWTISPV GSPNSQIGWG AGNVPVVLPP NNYVWTLTLT SGGYNIQDGK RTVSWSLNNA TAGEEVSIGA DATFSGRWVI EKV

Formula weight

16586.12 Da

Source organism

Coprinopsis cinerea

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.4 %, Completeness: 93.0 %, Completeness (bb): 93.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	93.0 % (1579 of 1697)	93.3 % (811 of 869)	92.0 % (611 of 664)	95.7 % (157 of 164)
Backbone	93.5 % (840 of 898)	93.6 % (292 of 312)	93.0 % (412 of 443)	95.1 % (136 of 143)
Sidechain	93.1 % (871 of 936)	93.2 % (519 of 557)	92.5 % (331 of 358)	100.0 % (21 of 21)
Aromatic	82.7 % (134 of 162)	90.1 % (73 of 81)	73.3 % (55 of 75)	100.0 % (6 of 6)
Methyl	98.2 % (163 of 166)	96.4 % (80 of 83)	100.0 % (83 of 83)

1. CCL2 (free)

MGHHHHHHHH SGDSPAVTLS AGNYIIYNRV LSPRGEKLAL TYPGRQRTPV TVSPLDGSSE QAWILRSYDS NSNTWTISPV GSPNSQIGWG AGNVPVVLPP NNYVWTLTLT SGGYNIQDGK RTVSWSLNNA TAGEEVSIGA DATFSGRWVI EKV

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 5.7

#	Name	Isotope labeling	Concentration
1	CCL2	[U-100% 13C; U-100% 15N]	1 mM
2	potassium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	100 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 310 K, pH 5.7

#	Name	Isotope labeling	Concentration
6	CCL2	[U-100% 13C; U-100% 15N]	1 mM
7	potassium phosphate	natural abundance	50 mM
8	sodium chloride	natural abundance	100 mM
9	D2O	natural abundance	100 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 5.7

#	Name	Isotope labeling	Concentration
10	CCL2	[U-100% 15N]	1 mM
11	potassium phosphate	natural abundance	50 mM
12	sodium chloride	natural abundance	100 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 310 K, pH 5.7

#	Name	Isotope labeling	Concentration
15	CCL2	[U-100% 15N]	1 mM
16	potassium phosphate	natural abundance	50 mM
17	sodium chloride	natural abundance	100 mM
18	D2O	natural abundance	100 %

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: -0.23 ppm, Outliers: 2 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: -0.23 ppm, Outliers: 2 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: -0.13 ppm, Outliers: 2 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: 0.42 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2012-06-03

Citation

Plasticity of the β-trefoil protein fold in the recognition and control of invertebrate predators and parasites by a fungal defence system
Schubert, M., Bleuler-Martinez, S., Butschi, A., Walti, M.A., Egloff, P., Stutz, K., Yan, S., Wilson, I.B.H., Hengartner, M.O., Aebi, M., Allain, F.H.-T., Kunzler, M.
PLoS Pathog. (2012), 8, e1002706-e1002706, PubMed 22615566 , DOI 10.1371/journal.ppat.1002706 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 17902 released on 2016-06-28
Title Solution structure of CCL2 in complex

Related entities 1. CCL2 (free), : 1 : 3 entities Detail

Experiments performed 1 experiments Detail

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17890_2lie.nef
Input source #2: Coordindates	2lie.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--------90-------100
MGHHHHHHHHSGDSPAVTLSAGNYIIYNRVLSPRGEKLALTYPGRQRTPVTVSPLDGSSEQAWILRSYDSNSNTWTISPVGSPNSQIGWGAGNVPVVLPP
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGHHHHHHHHSGDSPAVTLSAGNYIIYNRVLSPRGEKLALTYPGRQRTPVTVSPLDGSSEQAWILRSYDSNSNTWTISPVGSPNSQIGWGAGNVPVVLPP

-------110-------120-------130-------140-------150---
NNYVWTLTLTSGGYNIQDGKRTVSWSLNNATAGEEVSIGADATFSGRWVIEKV
|||||||||||||||||||||||||||||||||||||||||||||||||||||
NNYVWTLTLTSGGYNIQDGKRTVSWSLNNATAGEEVSIGADATFSGRWVIEKV

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	153	0	0	100.0

Content subtype: combined_17890_2lie.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	CCL2_free	Warning	1587		96.7 (chain: A, length: 153)
1	Distance restraints	AMBER_distance_constraints_2	Warning	3532 (1)	noe	90.8 (chain: A, length: 153)
2	Distance restraints	AMBER_distance_constraints_3	OK	92 (1)	hbond	36.6 (chain: A, length: 153)
1	Dihedral angle restraints	AMBER_dihedral_4	OK	186 (186)	.	81.7 (chain: A, length: 153)
2	Dihedral angle restraints	AMBER_dihedral_6	Warning	1 (1)	.	1.3 (chain: A, length: 153)

Assigned chemical shifts

Saveframe: CCL2_free
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 153, Sequence coverage: 96.7%
- Total number of assignments
  - ¹H chemical shifts: 821
  - ¹³C chemical shifts: 605
  - ¹⁵N chemical shifts: 161
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
71	ASN	CG	176.872
73	ASN	CG	179.157
84	ASN	CG	177.666
128	ASN	CG	176.37

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	869	821	94.5
¹³C chemical shifts	664	601	90.5
¹⁵N chemical shifts	171	161	94.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	312	296	94.9
¹³C chemical shifts	306	276	90.2
¹⁵N chemical shifts	143	133	93.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	557	525	94.3
¹³C chemical shifts	358	325	90.8
¹⁵N chemical shifts	28	28	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	84	84	100.0
¹³C chemical shifts	84	84	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	81	71	87.7
¹³C chemical shifts	75	51	68.0
¹⁵N chemical shifts	6	6	100.0

Distance restraints

Saveframe: AMBER_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 153, Sequence coverage: 90.8%
- Total number of restraints: 3427
- Weight of restraints: 1.0 (3427)
- Potential type of restraints: square-well-parabolic (3427)
- Range of distance target values: 2.4, 5.92 (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: AMBER_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 153, Sequence coverage: 36.6%
  - Total number of restraints: 92
  - Weight of restraints: 1.0 (92)
  - Potential type of restraints: square-well-parabolic (92)
  - Range of distance target values: 2.35, 3.15 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: AMBER_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 153, Sequence coverage: 81.7%
- Total number of restraints: 186
- Total number of restraints per polymer type: 186
- Weight of restraints: 1.0 (186)
- Potential type of restraints: square-well-parabolic (186)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
- Saveframe: AMBER_dihedral_6
  - Status: Warning
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 153, Sequence coverage: 1.3%
  - Total number of restraints: 1
  - Total number of restraints per polymer type: 1
  - Weight of restraints: 1.0 (1)
  - Potential type of restraints: square-well-parabolic (1)
  - Dihedral angle restraints per residue

Keywords lectin

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Found 1 Document (0.847 seconds)

BMRB: 17890

Sample #1

Sample #2

Sample #3

Sample #4

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. CCL2 (free), : 1 : 3 entities Detail

Experiments performed 1 experiments Detail

Instrument

Sample

NMR combined restraints 6 contents Detail