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BMRB: 19395

2MBC

Solution Structure of human holo-PRL-3 in complex with vanadate

Authors

Jeong, K., Kang, D., Kim, J., Shin, S., Jin, B., Lee, C., Kim, E., Jeon, Y.H., Kim, Y.

Assembly

human holo-PRL-3 in complex with vanadate

Entity

1. holo-PRL-3 in complex with vanadate (polymer), 162 monomers, 18240.04 Da Detail

MARMNRPAPV EVSYKHMRFL ITHNPTNATL STFIEDLKKY GATTVVRVCE VTYDKTPLEK DGITVVDWPF DDGAPPPGKV VEDWLSLVKA KFCEAPGSCV AVHCVAGLGR APVLVALALI ESGMKYEDAI QFIRQKRRGA INSKQLTYLE KYRPKQRLRF KD

2. (2S)-2-amino-3-methyl-1-{4-[3-(thiophen-2-yl)-1,2,4-oxadiazol-5-yl]piperidin-1-yl}butan-1-one (non-polymer), 334.436 × 5 Da
3. 4-[(E)-(4-hydroxynaphthalen-1-yl)diazenyl]benzenesulfonic acid (non-polymer), 328.342 Da

Total weight

20240.56 Da

Max. entity weight

18240.04 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 91.4 %, Completeness: 73.0 %, Completeness (bb): 75.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	73.0 % (1399 of 1916)	79.3 % (792 of 999)	62.2 % (470 of 756)	85.1 % (137 of 161)
Backbone	75.5 % (717 of 950)	88.2 % (284 of 322)	62.9 % (300 of 477)	88.1 % (133 of 151)
Sidechain	73.0 % (817 of 1119)	75.0 % (508 of 677)	70.6 % (305 of 432)	40.0 % (4 of 10)
Aromatic	18.8 % (27 of 144)	34.7 % (25 of 72)	0.0 % (0 of 70)	100.0 % (2 of 2)
Methyl	82.8 % (159 of 192)	83.3 % (80 of 96)	82.3 % (79 of 96)

1. holo-PRL-3 in complex with vanadate

MARMNRPAPV EVSYKHMRFL ITHNPTNATL STFIEDLKKY GATTVVRVCE VTYDKTPLEK DGITVVDWPF DDGAPPPGKV VEDWLSLVKA KFCEAPGSCV AVHCVAGLGR APVLVALALI ESGMKYEDAI QFIRQKRRGA INSKQLTYLE KYRPKQRLRF KD

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.3

#	Name	Isotope labeling	Type	Concentration
1	holo PRL-3 in complex with vanadate	natural abundance
2	HEPES	natural abundance		50 mM
3	NaCl	natural abundance		100 mM
4	DTT	natural abundance		10 mM
5	sodium orthovanadate	natural abundance		3 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

Protein Blocks Logo

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

Release date

2013-10-07

Citation

Structure of human PRL-3, the phosphatase associated with cancer metastasis
Kim, K., Song, J.H., Jee, J., Sheen, M.R., Lee, C., Lee, T.G., Ro, S., Cho, J.M., Lee, W., Yamazaki, T., Jeon, Y.H., Cheong, C.
FEBS Lett. (2004), 565, 181-187, PubMed 15135076 , DOI 10.1016/j.febslet.2004.03.062 , Abstract

Related entities 1. holo-PRL-3 in complex with vanadate, : 1 : 4 : 1 : 54 entities Detail

Interaction partners 1. holo-PRL-3 in complex with vanadate, : 109 interactors Detail

More details for 109 interactors identified by 3 citations

Experiments performed 10 experiments Detail

1 3D HNCACB

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.3

#	Name	Isotope labeling	Type	Concentration
1	holo PRL-3 in complex with vanadate	natural abundance
2	HEPES	natural abundance		50 mM
3	NaCl	natural abundance		100 mM
4	DTT	natural abundance		10 mM
5	sodium orthovanadate	natural abundance		3 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

2 3D CBCA(CO)NH

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.3

#	Name	Isotope labeling	Type	Concentration
1	holo PRL-3 in complex with vanadate	natural abundance
2	HEPES	natural abundance		50 mM
3	NaCl	natural abundance		100 mM
4	DTT	natural abundance		10 mM
5	sodium orthovanadate	natural abundance		3 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

3 3D HNCA

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.3

#	Name	Isotope labeling	Type	Concentration
1	holo PRL-3 in complex with vanadate	natural abundance
2	HEPES	natural abundance		50 mM
3	NaCl	natural abundance		100 mM
4	DTT	natural abundance		10 mM
5	sodium orthovanadate	natural abundance		3 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

4 3D HN(CO)CA

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.3

#	Name	Isotope labeling	Type	Concentration
1	holo PRL-3 in complex with vanadate	natural abundance
2	HEPES	natural abundance		50 mM
3	NaCl	natural abundance		100 mM
4	DTT	natural abundance		10 mM
5	sodium orthovanadate	natural abundance		3 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

5 3D HNHA

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.3

#	Name	Isotope labeling	Type	Concentration
1	holo PRL-3 in complex with vanadate	natural abundance
2	HEPES	natural abundance		50 mM
3	NaCl	natural abundance		100 mM
4	DTT	natural abundance		10 mM
5	sodium orthovanadate	natural abundance		3 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

6 3D HCCH-TOCSY

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.3

#	Name	Isotope labeling	Type	Concentration
1	holo PRL-3 in complex with vanadate	natural abundance
2	HEPES	natural abundance		50 mM
3	NaCl	natural abundance		100 mM
4	DTT	natural abundance		10 mM
5	sodium orthovanadate	natural abundance		3 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

7 3D C(CO)NH

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.3

#	Name	Isotope labeling	Type	Concentration
1	holo PRL-3 in complex with vanadate	natural abundance
2	HEPES	natural abundance		50 mM
3	NaCl	natural abundance		100 mM
4	DTT	natural abundance		10 mM
5	sodium orthovanadate	natural abundance		3 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

8 3D H(CCO)NH

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.3

#	Name	Isotope labeling	Type	Concentration
1	holo PRL-3 in complex with vanadate	natural abundance
2	HEPES	natural abundance		50 mM
3	NaCl	natural abundance		100 mM
4	DTT	natural abundance		10 mM
5	sodium orthovanadate	natural abundance		3 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

9 3D 1H-15N NOESY

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.3

#	Name	Isotope labeling	Type	Concentration
1	holo PRL-3 in complex with vanadate	natural abundance
2	HEPES	natural abundance		50 mM
3	NaCl	natural abundance		100 mM
4	DTT	natural abundance		10 mM
5	sodium orthovanadate	natural abundance		3 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

10 3D 1H-13C NOESY

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.3

#	Name	Isotope labeling	Type	Concentration
1	holo PRL-3 in complex with vanadate	natural abundance
2	HEPES	natural abundance		50 mM
3	NaCl	natural abundance		100 mM
4	DTT	natural abundance		10 mM
5	sodium orthovanadate	natural abundance		3 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_19395_2mbc.nef
Input source #2: Coordindates	2mbc.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	None
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)

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
MARMNRPAPVEVSYKHMRFLITHNPTNATLSTFIEDLKKYGATTVVRVCEVTYDKTPLEKDGITVVDWPFDDGAPPPGKVVEDWLSLVKAKFCEAPGSCV
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MARMNRPAPVEVSYKHMRFLITHNPTNATLSTFIEDLKKYGATTVVRVCEVTYDKTPLEKDGITVVDWPFDDGAPPPGKVVEDWLSLVKAKFCEAPGSCV

-------110-------120-------130-------140-------150-------160--
AVHCVAGLGRAPVLVALALIESGMKYEDAIQFIRQKRRGAINSKQLTYLEKYRPKQRLRFKD
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
AVHCVAGLGRAPVLVALALIESGMKYEDAIQFIRQKRRGAINSKQLTYLEKYRPKQRLRFKD

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	162	0	0	100.0

Content subtype: combined_19395_2mbc.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1318		87.7 (chain: A, length: 162)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	3093 (1)	noe	86.4 (chain: A, length: 162)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 162, Sequence coverage: 87.7%
- Total number of assignments
  - ¹H chemical shifts: 761
  - ¹³C chemical shifts: 427
  - ¹⁵N chemical shifts: 130
- 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

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 162, Sequence coverage: 86.4%
- Total number of restraints: 3093
- Weight of restraints: 1.0 (3093)
- Potential type of restraints: upper-bound-parabolic (3093)
- Range of distance target values: 2.29, 6.0 (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

Keywords holo-PRL-3, vanadate