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BMRB: 16480

2LGP

NMR solution structure of double module LA45 of LDLR

Authors

Guttman, M., Komives, E.A.

Assembly

LDLR

Entity

1. double module LA45 (polymer, Thiol state: all disulfide bound), 94 monomers, 10161.97 Da Detail

GSPVLTCGPA SFQCNSSTCI PQLWACDNDP DCEDGSDEWP QRCRGLYVFQ GDSSPCSAFE FHCLSGECIH SSWRCDGGPD CKDKSDEENC AVAT

2. CA (non-polymer), 40.078 × 2 Da

Total weight

10242.126 Da

Max. entity weight

10161.97 Da

Entity Connection

disulfide 6 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS7:SG	1:CYS19:SG
2	disulfide	sing	1:CYS14:SG	1:CYS32:SG
3	disulfide	sing	1:CYS26:SG	1:CYS43:SG
4	disulfide	sing	1:CYS56:SG	1:CYS68:SG
5	disulfide	sing	1:CYS63:SG	1:CYS81:SG
6	disulfide	sing	1:CYS75:SG	1:CYS90:SG

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

DGSA-distance geometry simulated annealing

Data set

assigned_chemical_shifts, heteronucl_NOEs, heteronucl_T1_relaxation, heteronucl_T2_relaxation

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 94.3 %, Completeness (bb): 93.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	94.3 % (933 of 989)	96.1 % (492 of 512)	91.8 % (349 of 380)	94.8 % (92 of 97)
Backbone	93.3 % (513 of 550)	94.2 % (178 of 189)	92.3 % (253 of 274)	94.3 % (82 of 87)
Sidechain	95.6 % (502 of 525)	97.2 % (314 of 323)	92.7 % (178 of 192)	100.0 % (10 of 10)
Aromatic	89.1 % (82 of 92)	100.0 % (46 of 46)	76.7 % (33 of 43)	100.0 % (3 of 3)
Methyl	84.6 % (44 of 52)	80.8 % (21 of 26)	88.5 % (23 of 26)

1. double module LA45

GSPVLTCGPA SFQCNSSTCI PQLWACDNDP DCEDGSDEWP QRCRGLYVFQ GDSSPCSAFE FHCLSGECIH SSWRCDGGPD CKDKSDEENC AVAT

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 307 K, pH 7.45

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	0.8 mM
2	HEPES	[U-99% 2H]	20 mM
3	sodium chloride	natural abundance	150 mM
4	sodium azide	natural abundance	3 mM
5	CALCIUM ION	natural abundance	10 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 307 K, pH 7.45

#	Name	Isotope labeling	Concentration
8	entity_1	[U-99% 13C; U-99% 15N]	0.8 mM
9	HEPES	[U-99% 2H]	20 mM
10	sodium chloride	natural abundance	150 mM
11	sodium azide	natural abundance	3 mM
12	CALCIUM ION	natural abundance	10 mM
13	D2O	natural abundance	100 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 307 K, pH 7.45

#	Name	Isotope labeling	Concentration
14	entity_1	[U-99% 15N]	0.8 mM
15	HEPES	[U-99% 2H]	20 mM
16	sodium chloride	natural abundance	150 mM
17	sodium azide	natural abundance	3 mM
18	CALCIUM ION	natural abundance	10 mM
19	H2O	natural abundance	90 %
20	D2O	natural abundance	10 %

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	external	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.13 ppm, Outliers: 3 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	external	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.13 ppm, Outliers: 3 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	external	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.05 ppm, Outliers: 1 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	external	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.21 ppm, Outliers: 4 Detail

Protein Blocks Logo

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

Heteronucl. T₁

72 T₁ values in 1 lists
Coherence Sz, Field strength (¹H) 600 MHz, Pressure 1 atm, Temperature 307 K, pH 7.45 Detail

Heteronucl. T₂

71 T₂ values in 1 lists
Coherence S(+,-), Field strength (¹H) 600 MHz, Pressure 1 atm, Temperature 307 K, pH 7.45 Detail

Heteronucl. NOE

69 NOE values in 1 lists
Value type relative intensities, Field strength (¹H) 600 MHz, Pressure 1 atm, Temperature 307 K, pH 7.45 Detail

Heteronucl. T₁/T₂

71 T₁/T₂ values in 1 lists
Field strength (¹H) 600 MHz, Pressure 1 atm, Temperature 307 K, pH 7.45 Detail

Release date

2009-11-03

Citation

Structure and dynamics of the forth and fifth ligand binding module pair from LDLR: more than just beads on a string
Guttman, M., Komives, E.A.
Not known

Related entities 1. double module LA45, : 1 : 4 : 772 entities Detail

Interaction partners 1. double module LA45, : 16 interactors Detail

More details for 16 interactors identified by 11 citations