BMRBj - BMREntryMaster

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BMRB: 19403

2MBK

The Clip-segment of the von Willebrand domain 1 of the BMP modulator protein Crossveinless 2 is preformed

Authors

Mueller, T.D., Fiebig, J.E., Weidauer, S.E., Qiu, L., Bauer, M., Schmieder, P., Beerbaum, M., Zhang, J., Oschkinat, H., Sebald, W.

Assembly

Clip-segment of the von Willebrand domain 1 of Crossveinless 2

Entity

1. Clip-segment of the von Willebrand domain 1 of Crossveinless 2 (polymer), 67 monomers, 7185.234 Da Detail

WLITGTEASC ENEGEVLHIP NITDNPCISC VCLNQKAECK QEKCAPLAED CALVVKQTGA CCEKCKG

Formula weight

7185.234 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 84.9 %, Completeness (bb): 99.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	84.9 % (618 of 728)	92.6 % (350 of 378)	73.0 % (203 of 278)	90.3 % (65 of 72)
Backbone	99.5 % (394 of 396)	100.0 % (135 of 135)	99.0 % (195 of 197)	100.0 % (64 of 64)
Sidechain	72.9 % (288 of 395)	88.5 % (215 of 243)	50.0 % (72 of 144)	12.5 % (1 of 8)
Aromatic	50.0 % (8 of 16)	100.0 % (8 of 8)	0.0 % (0 of 7)	0.0 % (0 of 1)
Methyl	65.3 % (47 of 72)	100.0 % (36 of 36)	30.6 % (11 of 36)

1. entity

WLITGTEASC ENEGEVLHIP NITDNPCISC VCLNQKAECK QEKCAPLAED CALVVKQTGA CCEKCKG

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 300 K, pH 6.6

#	Name	Isotope labeling	Type	Concentration
1	CV2 VWC1	[U-99% 13C; U-99% 15N]		2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		20 mM
4	D2O	[U-2H]		5 %
5	sodium azide	natural abundance		0.2 %
6	H2O	[U-2H]		95 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 300 K, pH 6.6

#	Name	Isotope labeling	Type	Concentration
7	CV2 VWC1	[U-99% 15N]		1.5 mM
8	sodium phosphate	natural abundance		20 mM
9	sodium chloride	natural abundance		20 mM
10	D2O	[U-2H]		5 %
11	sodium azide	natural abundance		0.2 %
12	H2O	[U-2H]		95 %

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 300 K, pH 6.6

#	Name	Isotope labeling	Type	Concentration
13	CV2 VWC1	natural abundance		2 mM
14	sodium phosphate	natural abundance		20 mM
15	sodium chloride	natural abundance		20 mM
16	D2O	[U-2H]		5 %
17	sodium azide	natural abundance		0.2 %
18	H2O	[U-2H]		95 %

LACS Plot; CA

Referencing offset: 0.24 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: 0.24 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: 0.09 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: -1.67 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2MBK, Strand ID: A Detail

Release date

2013-10-13

Citation

The clip-segment of the von Willebrand domain 1 of the BMP modulator protein Crossveinless 2 is preformed
Fiebig, J.E., Weidauer, S.E., Qiu, L., Bauer, M., Schmieder, P., Beerbaum, M., Zhang, J., Oschkinat, H., Sebald, W., Mueller, T.D.
Molecules (2013), 18, 11658-11682, PubMed 24071977 , DOI 10.3390/molecules181011658 , Abstract

Related entities 1. Clip-segment of the von Willebrand domain 1 of Crossveinless 2, : 1 : 1 : 1 : 57 entities Detail

Experiments performed 11 experiments Detail

1 2D 1H-1H TOCSY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 300 K, pH 6.6

#	Name	Isotope labeling	Type	Concentration
13	CV2 VWC1	natural abundance		2 mM
14	sodium phosphate	natural abundance		20 mM
15	sodium chloride	natural abundance		20 mM
16	D2O	[U-2H]		5 %
17	sodium azide	natural abundance		0.2 %
18	H2O	[U-2H]		95 %

2 2D DQF-COSY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 300 K, pH 6.6

#	Name	Isotope labeling	Type	Concentration
13	CV2 VWC1	natural abundance		2 mM
14	sodium phosphate	natural abundance		20 mM
15	sodium chloride	natural abundance		20 mM
16	D2O	[U-2H]		5 %
17	sodium azide	natural abundance		0.2 %
18	H2O	[U-2H]		95 %

3 2D 1H-1H NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 300 K, pH 6.6

#	Name	Isotope labeling	Type	Concentration
13	CV2 VWC1	natural abundance		2 mM
14	sodium phosphate	natural abundance		20 mM
15	sodium chloride	natural abundance		20 mM
16	D2O	[U-2H]		5 %
17	sodium azide	natural abundance		0.2 %
18	H2O	[U-2H]		95 %

4 3D 1H-15N NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 300 K, pH 6.6

#	Name	Isotope labeling	Type	Concentration
7	CV2 VWC1	[U-99% 15N]		1.5 mM
8	sodium phosphate	natural abundance		20 mM
9	sodium chloride	natural abundance		20 mM
10	D2O	[U-2H]		5 %
11	sodium azide	natural abundance		0.2 %
12	H2O	[U-2H]		95 %

5 3D 1H-15N TOCSY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 300 K, pH 6.6

#	Name	Isotope labeling	Type	Concentration
7	CV2 VWC1	[U-99% 15N]		1.5 mM
8	sodium phosphate	natural abundance		20 mM
9	sodium chloride	natural abundance		20 mM
10	D2O	[U-2H]		5 %
11	sodium azide	natural abundance		0.2 %
12	H2O	[U-2H]		95 %

6 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 300 K, pH 6.6

#	Name	Isotope labeling	Type	Concentration
1	CV2 VWC1	[U-99% 13C; U-99% 15N]		2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		20 mM
4	D2O	[U-2H]		5 %
5	sodium azide	natural abundance		0.2 %
6	H2O	[U-2H]		95 %

7 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 300 K, pH 6.6

#	Name	Isotope labeling	Type	Concentration
1	CV2 VWC1	[U-99% 13C; U-99% 15N]		2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		20 mM
4	D2O	[U-2H]		5 %
5	sodium azide	natural abundance		0.2 %
6	H2O	[U-2H]		95 %

8 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 300 K, pH 6.6

#	Name	Isotope labeling	Type	Concentration
1	CV2 VWC1	[U-99% 13C; U-99% 15N]		2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		20 mM
4	D2O	[U-2H]		5 %
5	sodium azide	natural abundance		0.2 %
6	H2O	[U-2H]		95 %

9 3D HN(CA)CO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 300 K, pH 6.6

#	Name	Isotope labeling	Type	Concentration
1	CV2 VWC1	[U-99% 13C; U-99% 15N]		2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		20 mM
4	D2O	[U-2H]		5 %
5	sodium azide	natural abundance		0.2 %
6	H2O	[U-2H]		95 %

10 3D HBHA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 300 K, pH 6.6

#	Name	Isotope labeling	Type	Concentration
1	CV2 VWC1	[U-99% 13C; U-99% 15N]		2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		20 mM
4	D2O	[U-2H]		5 %
5	sodium azide	natural abundance		0.2 %
6	H2O	[U-2H]		95 %

11 3D H(CCO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 300 K, pH 6.6

#	Name	Isotope labeling	Type	Concentration
1	CV2 VWC1	[U-99% 13C; U-99% 15N]		2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		20 mM
4	D2O	[U-2H]		5 %
5	sodium azide	natural abundance		0.2 %
6	H2O	[U-2H]		95 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_19403_2mbk.nef
Input source #2: Coordindates	2mbk.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	Error

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:9:CYS:SG	A:31:CYS:SG	oxidized, CA 54.24, CB 45.91 ppm	oxidized, CA 55.11, CB 41.38 ppm	2.028
A:26:CYS:SG	A:60:CYS:SG	oxidized, CA 54.76, CB 42.09 ppm	oxidized, CA 58.15, CB 41.83 ppm	2.028
A:29:CYS:SG	A:38:CYS:SG	oxidized, CA 55.02, CB 49.73 ppm	oxidized, CA 54.98, CB 47.0 ppm	2.024
A:43:CYS:SG	A:61:CYS:SG	oxidized, CA 53.09, CB 37.9 ppm	oxidized, CA 52.51, CB 39.4 ppm	2.03
A:50:CYS:SG	A:64:CYS:SG	oxidized, CA 57.62, CB 42.0 ppm	oxidized, CA 55.94, CB 42.95 ppm	2.017

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

None

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	0	.	Not matched with CCD	None

Sequence alignments

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

---                                                                   
.GS                                                                   
 ||                                                                   
-GSWLITGTEASCENEGEVLHIPNITDNPCISCVCLNQKAECKQEKCAPLAEDCALVVKQTGACCEKCKG
 ---------10--------20--------30--------40--------50--------60--------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	69	1	0	100.0

Content subtype: combined_19403_2mbk.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	Warning	5		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	605		No information
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Error	1029 (1)	noe	94.3 (chain: A, length: 70)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning

Covalent bonds

Saveframe: assembly
- Status: Warning

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Error
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 70, Sequence coverage: 94.3%
- Total number of restraints: 1029
- Weight of restraints: 1.0 (1029)
- Potential type of restraints: square-well-parabolic (1029)
- Range of distance target values: 2.4, 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

Keywords BMPER, BMP modulator, Crossveinless 2, von Willebrand type C domain