BMRBj - BMREntryMaster

Found 1 Document (1.375 seconds)

BMRB: 17477

2L9L

NMR Structure of the Mouse MFG-E8 C2 Domain

Authors

Ye, H., Subramanian, V., Yu, L., Yoon, H.

Assembly

Mouse MFG-E8 C2 Domain

Entity

1. Mouse MFG-E8 C2 Domain (polymer), 170 monomers, 19407.49 Da Detail

MKSGHGCSEP LGLKNNTIPD SQMSASSSYK TWNLRAFGWY PHLGRLDNQG KINAWTAQSN SAKEWLQVDL GTQRQVTGII TQGARDFGHI QYVASYKVAH SDDGVQWTVY EEQGSSKVFQ GNLDNNSHKK NIFEKPFMAR YVRVLPVSWH NRITLRLELL GCLEHHHHHH

Formula weight

19407.49 Da

Source organism

Mus musculus

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 93.5 %, Completeness: 78.9 %, Completeness (bb): 91.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	78.9 % (1583 of 2006)	80.1 % (835 of 1043)	75.6 % (582 of 770)	86.0 % (166 of 193)
Backbone	91.8 % (927 of 1010)	92.8 % (324 of 349)	90.7 % (450 of 496)	92.7 % (153 of 165)
Sidechain	69.4 % (800 of 1152)	73.6 % (511 of 694)	64.2 % (276 of 430)	46.4 % (13 of 28)
Aromatic	11.0 % (24 of 218)	18.3 % (20 of 109)	0.0 % (0 of 103)	66.7 % (4 of 6)
Methyl	93.0 % (147 of 158)	97.5 % (77 of 79)	88.6 % (70 of 79)

1. MFG-E8 C2 domain

MKSGHGCSEP LGLKNNTIPD SQMSASSSYK TWNLRAFGWY PHLGRLDNQG KINAWTAQSN SAKEWLQVDL GTQRQVTGII TQGARDFGHI QYVASYKVAH SDDGVQWTVY EEQGSSKVFQ GNLDNNSHKK NIFEKPFMAR YVRVLPVSWH NRITLRLELL GCLEHHHHHH

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	20 mM
2	sodium chloride	natural abundance	20 mM
3	sodium azide	natural abundance	0.01 %
4	MFG-E8 C2 domain	[U-13C; U-15N]	0.8 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
7	sodium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	20 mM
9	sodium azide	natural abundance	0.01 %
10	MFG-E8 C2 domain	[U-13C; U-15N]	0.8 mM
11	D2O	natural abundance	100 %

LACS Plot; CA

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

Referencing offset: 2.96 ppm, Outliers: 3 Detail

LACS Plot; CB

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

Referencing offset: 2.96 ppm, Outliers: 3 Detail

LACS Plot; HA

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

Referencing offset: 0.02 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: 3.5 ppm, Outliers: 5 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2L9L, Strand ID: A Detail

Release date

2012-08-30

Citation

NMR solution structure of C2 domain of MFG-E8 and insights into its molecular recognition with phosphatidylserine
Ye, H., Li, B., Subramanian, V., Choi, B., Yu, L., Harikishore, A., Harikishore, A., Chakraborty, G., Baek, K., Yoon, H.
Biochim. Biophys. Acta (2013), 1828, 1083-1093, PubMed 23262193 , DOI 10.1016/j.bbamem.2012.12.009 , Abstract

Related entities 1. Mouse MFG-E8 C2 Domain, : 1 : 2 : 309 entities Detail

Interaction partners 1. Mouse MFG-E8 C2 Domain, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	20 mM
2	sodium chloride	natural abundance	20 mM
3	sodium azide	natural abundance	0.01 %
4	MFG-E8 C2 domain	[U-13C; U-15N]	0.8 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

2 3D HNCACB

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	20 mM
2	sodium chloride	natural abundance	20 mM
3	sodium azide	natural abundance	0.01 %
4	MFG-E8 C2 domain	[U-13C; U-15N]	0.8 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	20 mM
2	sodium chloride	natural abundance	20 mM
3	sodium azide	natural abundance	0.01 %
4	MFG-E8 C2 domain	[U-13C; U-15N]	0.8 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

4 3D HNCA

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	20 mM
2	sodium chloride	natural abundance	20 mM
3	sodium azide	natural abundance	0.01 %
4	MFG-E8 C2 domain	[U-13C; U-15N]	0.8 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

5 3D HNCO

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	20 mM
2	sodium chloride	natural abundance	20 mM
3	sodium azide	natural abundance	0.01 %
4	MFG-E8 C2 domain	[U-13C; U-15N]	0.8 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

6 3D H(CC)(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	20 mM
2	sodium chloride	natural abundance	20 mM
3	sodium azide	natural abundance	0.01 %
4	MFG-E8 C2 domain	[U-13C; U-15N]	0.8 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

7 3D (H)CC(CO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	20 mM
2	sodium chloride	natural abundance	20 mM
3	sodium azide	natural abundance	0.01 %
4	MFG-E8 C2 domain	[U-13C; U-15N]	0.8 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

8 3D HCCH-TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
7	sodium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	20 mM
9	sodium azide	natural abundance	0.01 %
10	MFG-E8 C2 domain	[U-13C; U-15N]	0.8 mM
11	D2O	natural abundance	100 %

9 3D 1H-15N NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	20 mM
2	sodium chloride	natural abundance	20 mM
3	sodium azide	natural abundance	0.01 %
4	MFG-E8 C2 domain	[U-13C; U-15N]	0.8 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

10 3D 1H-13C NOESY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
7	sodium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	20 mM
9	sodium azide	natural abundance	0.01 %
10	MFG-E8 C2 domain	[U-13C; U-15N]	0.8 mM
11	D2O	natural abundance	100 %

11 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Concentration
7	sodium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	20 mM
9	sodium azide	natural abundance	0.01 %
10	MFG-E8 C2 domain	[U-13C; U-15N]	0.8 mM
11	D2O	natural abundance	100 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17477_2l9l.nef
Input source #2: Coordindates	2l9l.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:1:CYS:SG	A:156:CYS:SG	oxidized, CA 53.315, CB 42.748 ppm	oxidized, CA 52.123, CB 39.08 ppm	2.026

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----
MKSGHGCSEPLGLKNNTIPDSQMSASSSYKTWNLRAFGWYPHLGRLDNQGKINAWTAQSNSAKEWLQVDLGTQRQVTGIITQGARDFGHIQYVASYKVAH
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MKSGHGCSEPLGLKNNTIPDSQMSASSSYKTWNLRAFGWYPHLGRLDNQGKINAWTAQSNSAKEWLQVDLGTQRQVTGIITQGARDFGHIQYVASYKVAH
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

---100-------110-------120-------130-------140-------150-------160----
SDDGVQWTVYEEQGSSKVFQGNLDNNSHKKNIFEKPFMARYVRVLPVSWHNRITLRLELLGCLEHHHHHH
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SDDGVQWTVYEEQGSSKVFQGNLDNNSHKKNIFEKPFMARYVRVLPVSWHNRITLRLELLGCLEHHHHHH
-------110-------120-------130-------140-------150-------160-------170

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	170	0	0	100.0

Content subtype: combined_17477_2l9l.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1554		91.8 (chain: A, length: 170)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	2873 (1)	noe	88.8 (chain: A, length: 170)
2	Distance restraints	DYANA/DIANA_distance_constraints_5	Warning	6 (1)	disulfide_bond	1.2 (chain: A, length: 170)
3	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	198 (1)	hbond	31.8 (chain: A, length: 170)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	Warning	110 (56)	.	68.8 (chain: A, length: 170)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 170, Sequence coverage: 91.8%
- Total number of assignments
  - ¹H chemical shifts: 821
  - ¹³C chemical shifts: 573
  - ¹⁵N chemical shifts: 160
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
86	TYR	HH	8.886
122	HIS	HD1	6.658

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1043	819	78.5
¹³C chemical shifts	770	573	74.4
¹⁵N chemical shifts	201	160	79.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	349	319	91.4
¹³C chemical shifts	340	304	89.4
¹⁵N chemical shifts	165	149	90.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	694	500	72.0
¹³C chemical shifts	430	269	62.6
¹⁵N chemical shifts	36	11	30.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	82	76	92.7
¹³C chemical shifts	82	71	86.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	109	20	18.3
¹³C chemical shifts	103	0	0.0
¹⁵N chemical shifts	6	4	66.7

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 170, Sequence coverage: 88.8%
- Total number of restraints: 2873
- Weight of restraints: 1.0 (2873)
- Potential type of restraints: upper-bound-parabolic (2873)
- Range of distance target values: 2.32, 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_5
  - Status: Warning
  - Experiment type: disulfide_bond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 170, Sequence coverage: 1.2%
  - Total number of restraints: 6
  - Weight of restraints: 1.0 (6)
  - Potential type of restraints: upper-bound-parabolic (6)
  - Range of distance target values: 2.04, 3.1 (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_4
    - Status: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 170, Sequence coverage: 31.8%
    - Total number of restraints: 198
    - Weight of restraints: 1.0 (198)
    - Potential type of restraints: upper-bound-parabolic (198)
    - Range of distance target values: 1.8, 3.0 (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

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 170, Sequence coverage: 68.8%
- Total number of restraints: 56
- Total number of restraints per polymer type: 56
- Weight of restraints: 1.0 (56)
- Potential type of restraints: square-well-parabolic (56)
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords PROTEIN

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (1.375 seconds)

BMRB: 17477

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Mouse MFG-E8 C2 Domain, : 1 : 2 : 309 entities Detail

Interaction partners 1. Mouse MFG-E8 C2 Domain, : 1 interactors Detail

Experiments performed 11 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 6 contents Detail