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Found 1 Document (0.694 seconds)

BMRB: 18778

2LZU

Solution structure of LIMD2

Authors

Talebzadeh Farooji, M., Peng, H., Rauscher, F.J., Borden, K.KL., Osborne, M.J.

Assembly

LIMD2

Entity

1. LIMD2 (polymer, Thiol state: all free), 72 monomers, 8303.533 Da Detail

RAQVKETCAA CQKTVYPMER LVADKLIFHN SCFCCKHCHT KLSLGSYAAL HGEFYCKPHF QQLFKSKGNY DE

2. ZINC ION (non-polymer, Thiol state: not present), 65.409 × 2 Da

Total weight

8434.352 Da

Max. entity weight

8303.533 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 64.2 %, Completeness (bb): 68.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	64.2 % (553 of 861)	70.6 % (317 of 449)	51.2 % (172 of 336)	84.2 % (64 of 76)
Backbone	68.2 % (292 of 428)	82.1 % (119 of 145)	51.2 % (109 of 213)	91.4 % (64 of 70)
Sidechain	63.3 % (318 of 502)	65.1 % (198 of 304)	62.5 % (120 of 192)	0.0 % (0 of 6)
Aromatic	44.1 % (45 of 102)	88.2 % (45 of 51)	0.0 % (0 of 51)
Methyl	87.9 % (51 of 58)	89.7 % (26 of 29)	86.2 % (25 of 29)

1. LIMD2

RAQVKETCAA CQKTVYPMER LVADKLIFHN SCFCCKHCHT KLSLGSYAAL HGEFYCKPHF QQLFKSKGNY DE

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
1	LIMD2	[U-99% 13C; U-99% 15N]	300.0 ~ 500.0 uM
2	sodium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
7	LIMD2	[U-99% 15N]	300.0 ~ 500.0 uM
8	sodium phosphate	natural abundance	50 mM
9	sodium chloride	natural abundance	100 mM
10	TCEP	natural abundance	1 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
13	LIMD2	natural abundance	300.0 ~ 500.0 uM
14	sodium phosphate	natural abundance	50 mM
15	sodium chloride	natural abundance	100 mM
16	TCEP	natural abundance	1 mM
17	D2O	natural abundance	100 %

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
18	LIMD2	[U-99% 13C; U-99% 15N]	300.0 ~ 500.0 uM
19	sodium phosphate	natural abundance	50 mM
20	sodium chloride	natural abundance	100 mM
21	TCEP	natural abundance	1 mM
22	D2O	natural abundance	100 %

LACS Plot; CA

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

Referencing offset: 0.28 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: 0.28 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: 0.04 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2014-04-13

Citation

LIMD2 is a small LIM-only protein overexpressed in metastatic lesions that regulates cell motility and tumor progression by directly binding to and activating the integrin-linked kinase
Talebzadeh Farooji, M.
Cancer. Res. (2014), 74, 1390-1403, PubMed 24590809 , DOI 10.1158/0008-5472.CAN-13-1275 , Abstract

Related entities 1. LIMD2, : 1 : 2 : 5 : 247 entities Detail

Interaction partners 1. LIMD2, : 2 interactors Detail

More details for 2 interactors identified by 2 citations

Experiments performed 13 experiments Detail

1 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
1	LIMD2	[U-99% 13C; U-99% 15N]	300.0 ~ 500.0 uM
2	sodium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

2 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
7	LIMD2	[U-99% 15N]	300.0 ~ 500.0 uM
8	sodium phosphate	natural abundance	50 mM
9	sodium chloride	natural abundance	100 mM
10	TCEP	natural abundance	1 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

3 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
1	LIMD2	[U-99% 13C; U-99% 15N]	300.0 ~ 500.0 uM
2	sodium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

4 2D DQF-COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
13	LIMD2	natural abundance	300.0 ~ 500.0 uM
14	sodium phosphate	natural abundance	50 mM
15	sodium chloride	natural abundance	100 mM
16	TCEP	natural abundance	1 mM
17	D2O	natural abundance	100 %

5 2D 1H-1H TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
13	LIMD2	natural abundance	300.0 ~ 500.0 uM
14	sodium phosphate	natural abundance	50 mM
15	sodium chloride	natural abundance	100 mM
16	TCEP	natural abundance	1 mM
17	D2O	natural abundance	100 %

6 2D 1H-1H NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
13	LIMD2	natural abundance	300.0 ~ 500.0 uM
14	sodium phosphate	natural abundance	50 mM
15	sodium chloride	natural abundance	100 mM
16	TCEP	natural abundance	1 mM
17	D2O	natural abundance	100 %

7 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
18	LIMD2	[U-99% 13C; U-99% 15N]	300.0 ~ 500.0 uM
19	sodium phosphate	natural abundance	50 mM
20	sodium chloride	natural abundance	100 mM
21	TCEP	natural abundance	1 mM
22	D2O	natural abundance	100 %

8 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
7	LIMD2	[U-99% 15N]	300.0 ~ 500.0 uM
8	sodium phosphate	natural abundance	50 mM
9	sodium chloride	natural abundance	100 mM
10	TCEP	natural abundance	1 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

9 3D 1H-13C NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
18	LIMD2	[U-99% 13C; U-99% 15N]	300.0 ~ 500.0 uM
19	sodium phosphate	natural abundance	50 mM
20	sodium chloride	natural abundance	100 mM
21	TCEP	natural abundance	1 mM
22	D2O	natural abundance	100 %

10 3D H(CCO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
1	LIMD2	[U-99% 13C; U-99% 15N]	300.0 ~ 500.0 uM
2	sodium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

11 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
1	LIMD2	[U-99% 13C; U-99% 15N]	300.0 ~ 500.0 uM
2	sodium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

12 3D HBHA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
1	LIMD2	[U-99% 13C; U-99% 15N]	300.0 ~ 500.0 uM
2	sodium phosphate	natural abundance	50 mM
3	sodium chloride	natural abundance	100 mM
4	TCEP	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

13 3D HNHB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.2

#	Name	Isotope labeling	Concentration
7	LIMD2	[U-99% 15N]	300.0 ~ 500.0 uM
8	sodium phosphate	natural abundance	50 mM
9	sodium chloride	natural abundance	100 mM
10	TCEP	natural abundance	1 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_18778_2lzu.nef
Input source #2: Coordindates	2lzu.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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:59:HIS:ND1	2:2:ZN:ZN	unknown	unknown	n/a
1:29:HIS:ND1	2:1:ZN:ZN	unknown	unknown	n/a
1:8:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:11:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:32:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:38:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:35:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a
1:56:CYS:SG	2:2:ZN:ZN	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	ZN	ZINC ION	None
B	2	ZN	ZINC ION	None

Sequence alignments

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

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

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	72	0	0	100.0

Content subtype: combined_18778_2lzu.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	8		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	542		100.0 (chain: A, length: 72)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1207 (1)	noe	90.3 (chain: A, length: 72)
2	Distance restraints	CNS/XPLOR_distance_constraints_5	Warning	302 (1)	noe	76.4 (chain: A, length: 72)
3	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	24 (1)	hbond	25.0 (chain: A, length: 72)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 72, Sequence coverage: 100.0%
- Total number of assignments
  - ¹³C chemical shifts: 161
  - ¹H chemical shifts: 317
  - ¹⁵N chemical shifts: 64
- 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 (%)
¹³C chemical shifts	336	161	47.9
¹H chemical shifts	449	317	70.6
¹⁵N chemical shifts	78	64	82.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	144	49	34.0
¹H chemical shifts	145	119	82.1
¹⁵N chemical shifts	70	64	91.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	192	112	58.3
¹H chemical shifts	304	198	65.1
¹⁵N chemical shifts	8	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	30	21	70.0
¹H chemical shifts	30	26	86.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	51	0	0.0
¹H chemical shifts	51	45	88.2

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 72, Sequence coverage: 90.3%
- Total number of restraints: 1181
- Weight of restraints: 1.0 (1181)
- Potential type of restraints: square-well-parabolic (1181)
- Range of distance target values: 1.5, 4.27 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_5
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 72, Sequence coverage: 76.4%
  - Total number of restraints: 273
  - Weight of restraints: 1.0 (273)
  - Potential type of restraints: square-well-parabolic (273)
  - Range of distance target values: 1.71, 4.45 (Å)
  - Histogram of distance target values
  - Histogram of discrepancy in distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_4
    - Status: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 72, Sequence coverage: 25.0%
    - Total number of restraints: 24
    - Weight of restraints: 1.0 (24)
    - Potential type of restraints: square-well-parabolic (24)
    - Range of distance target values: 2.05, 3.05 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
        None
    - Distance restraints on contact map

Keywords LIMD2

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BMRB: 18778

Sample #1

Sample #2

Sample #3

Sample #4

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. LIMD2, : 1 : 2 : 5 : 247 entities Detail

Interaction partners 1. LIMD2, : 2 interactors Detail

Experiments performed 13 experiments Detail

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NMR combined restraints 5 contents Detail