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Found 1 Document (0.958 seconds)

BMRB: 18540

2LUT

NMR solution structure of midkine-a

Authors

Lim, J., Yang, D., Meng, D.

Assembly

midkine-a

Entity

1. midkine-a (polymer, Thiol state: all disulfide bound), 125 monomers, 13521.28 Da Detail

GSKNKKEKNK GGKGGADCAE WLYGSCVANN GDCGQGMREG TCNEQTRKVK CRVPCNWKKE FGADCKYKFG NWGECDAATS TKSRTGTLQK ALFNVECQQT VSVTKPCTTK VKNKPKGKKG KGKGN

Formula weight

13521.28 Da

Entity Connection

disulfide 5 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS18:SG	1:CYS42:SG
2	disulfide	sing	1:CYS26:SG	1:CYS51:SG
3	disulfide	sing	1:CYS33:SG	1:CYS55:SG
4	disulfide	sing	1:CYS65:SG	1:CYS97:SG
5	disulfide	sing	1:CYS75:SG	1:CYS107:SG

Source organism

Danio rerio

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.4 %, Completeness: 75.8 %, Completeness (bb): 79.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	75.8 % (1077 of 1421)	75.5 % (571 of 756)	72.6 % (381 of 525)	89.3 % (125 of 140)
Backbone	79.0 % (588 of 744)	90.6 % (240 of 265)	66.1 % (236 of 357)	91.8 % (112 of 122)
Sidechain	75.3 % (590 of 784)	67.4 % (331 of 491)	89.5 % (246 of 275)	72.2 % (13 of 18)
Aromatic	87.8 % (72 of 82)	87.8 % (36 of 41)	86.8 % (33 of 38)	100.0 % (3 of 3)
Methyl	100.0 % (74 of 74)	100.0 % (37 of 37)	100.0 % (37 of 37)

1. midkine-a

GSKNKKEKNK GGKGGADCAE WLYGSCVANN GDCGQGMREG TCNEQTRKVK CRVPCNWKKE FGADCKYKFG NWGECDAATS TKSRTGTLQK ALFNVECQQT VSVTKPCTTK VKNKPKGKKG KGKGN

Show sample condition

Sample

Solvent system 95%H2O, 5 % D2O, Pressure 1 atm, Temperature 303 K, pH 6.5, Details 10 mM NaH2PO4/ Na2HPO4 at pH 6.5, 0.1 mM NaN3, 100 mM NaCl, 1 mM EDTA, 95%H2O, 5 % D2O

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	10 mM
2	sodium azide	natural abundance	0.1 mM
3	sodium chloride	natural abundance	100 mM
4	EDTA	natural abundance	1 mM
5	midkine-a	[U-100% 13C; U-100% 15N]	0.8 mM
6	H2O	natural abundance	95 %
7	D2O	natural abundance	5 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.0 ppm	na	indirect	0.2514495
¹H	water	protons	4.71 ppm	external	indirect	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	na	indirect	0.1013291

Referencing offset: 0.49 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.0 ppm	na	indirect	0.2514495
¹H	water	protons	4.71 ppm	external	indirect	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	na	indirect	0.1013291

Referencing offset: 0.49 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.0 ppm	na	indirect	0.2514495
¹H	water	protons	4.71 ppm	external	indirect	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	na	indirect	0.1013291

Referencing offset: 0.04 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2013-04-01

Citation

Structure-function analysis of full-length midkine reveals novel residues important for heparin binding and zebrafish embryogenesis
Lim, J., Yao, S., Graf, M., Winkler, C., Yang, D.
Biochem. J. (2013), 451, 407-415, PubMed 23418741 , DOI 10.1042/BJ20121622 , Abstract

Related entities 1. midkine-a, : 1 : 10 entities Detail

Experiments performed 6 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95%H2O, 5 % D2O, Pressure 1 atm, Temperature 303 K, pH 6.5, Details 10 mM NaH2PO4/ Na2HPO4 at pH 6.5, 0.1 mM NaN3, 100 mM NaCl, 1 mM EDTA, 95%H2O, 5 % D2O

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	10 mM
2	sodium azide	natural abundance	0.1 mM
3	sodium chloride	natural abundance	100 mM
4	EDTA	natural abundance	1 mM
5	midkine-a	[U-100% 13C; U-100% 15N]	0.8 mM
6	H2O	natural abundance	95 %
7	D2O	natural abundance	5 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	10 mM
2	sodium azide	natural abundance	0.1 mM
3	sodium chloride	natural abundance	100 mM
4	EDTA	natural abundance	1 mM
5	midkine-a	[U-100% 13C; U-100% 15N]	0.8 mM
6	H2O	natural abundance	95 %
7	D2O	natural abundance	5 %

3 3D HN(CO)CA

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	10 mM
2	sodium azide	natural abundance	0.1 mM
3	sodium chloride	natural abundance	100 mM
4	EDTA	natural abundance	1 mM
5	midkine-a	[U-100% 13C; U-100% 15N]	0.8 mM
6	H2O	natural abundance	95 %
7	D2O	natural abundance	5 %

4 3D HNCA

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	10 mM
2	sodium azide	natural abundance	0.1 mM
3	sodium chloride	natural abundance	100 mM
4	EDTA	natural abundance	1 mM
5	midkine-a	[U-100% 13C; U-100% 15N]	0.8 mM
6	H2O	natural abundance	95 %
7	D2O	natural abundance	5 %

5 3D MQ-(H)CCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	10 mM
2	sodium azide	natural abundance	0.1 mM
3	sodium chloride	natural abundance	100 mM
4	EDTA	natural abundance	1 mM
5	midkine-a	[U-100% 13C; U-100% 15N]	0.8 mM
6	H2O	natural abundance	95 %
7	D2O	natural abundance	5 %

6 13C/ 15N edited-NOESY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	sodium phosphate	natural abundance	10 mM
2	sodium azide	natural abundance	0.1 mM
3	sodium chloride	natural abundance	100 mM
4	EDTA	natural abundance	1 mM
5	midkine-a	[U-100% 13C; U-100% 15N]	0.8 mM
6	H2O	natural abundance	95 %
7	D2O	natural abundance	5 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18540_2lut.nef
Input source #2: Coordindates	2lut.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:18:CYS:SG	A:42:CYS:SG	oxidized, CA 56.914, CB 42.32 ppm	oxidized, CA 54.955, CB 39.219 ppm	2.119
A:26:CYS:SG	A:51:CYS:SG	oxidized, CA 55.777, CB 41.304 ppm	oxidized, CA 54.486, CB 45.921 ppm	1.986
A:33:CYS:SG	A:55:CYS:SG	oxidized, CA 55.885, CB 47.24 ppm	unknown, CA 53.258 ppm	2.126
A:65:CYS:SG	A:97:CYS:SG	oxidized, CA 53.149, CB 42.646 ppm	oxidized, CA 53.772, CB 44.152 ppm	2.001
A:75:CYS:SG	A:107:CYS:SG	oxidized, CA 56.051, CB 40.212 ppm	oxidized, CA 54.701, CB 44.237 ppm	2.139

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
GSKNKKEKNKGGKGGADCAEWLYGSCVANNGDCGQGMREGTCNEQTRKVKCRVPCNWKKEFGADCKYKFGNWGECDAATSTKSRTGTLQKALFNVECQQT
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSKNKKEKNKGGKGGADCAEWLYGSCVANNGDCGQGMREGTCNEQTRKVKCRVPCNWKKEFGADCKYKFGNWGECDAATSTKSRTGTLQKALFNVECQQT

-------110-------120-----
VSVTKPCTTKVKNKPKGKKGKGKGN
|||||||||||||||||||||||||
VSVTKPCTTKVKNKPKGKKGKGKGN

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	125	0	0	100.0

Content subtype: combined_18540_2lut.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	5		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1043		96.8 (chain: A, length: 125)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	3738 (1)	noe	87.2 (chain: A, length: 125)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	108 (108)	.	64.0 (chain: A, length: 125)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 125, Sequence coverage: 96.8%
- Total number of assignments
  - ¹H chemical shifts: 554
  - ¹³C chemical shifts: 367
  - ¹⁵N chemical shifts: 122
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	756	553	73.1
¹³C chemical shifts	525	367	69.9
¹⁵N chemical shifts	144	122	84.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	265	239	90.2
¹³C chemical shifts	250	121	48.4
¹⁵N chemical shifts	122	109	89.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	491	314	64.0
¹³C chemical shifts	275	246	89.5
¹⁵N chemical shifts	22	13	59.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	38	37	97.4
¹³C chemical shifts	38	37	97.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	41	36	87.8
¹³C chemical shifts	38	33	86.8
¹⁵N chemical shifts	3	3	100.0

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: 125, Sequence coverage: 87.2%
- Total number of restraints: 3738
- Weight of restraints: 1.0 (3738)
- Potential type of restraints: upper-bound-parabolic (3738)
- Range of distance target values: 1.8, 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

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 125, Sequence coverage: 64.0%
- Total number of restraints: 108
- Total number of restraints per polymer type: 108
- Weight of restraints: 1.0 (108)
- Potential type of restraints: square-well-parabolic (108)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords beta sheet, disulfide bond, independent half-domains, midkine

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Found 1 Document (0.958 seconds)

BMRB: 18540

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. midkine-a, : 1 : 10 entities Detail

Experiments performed 6 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail