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Found 1 Document (1.783 seconds)

BMRB: 15922

2K7N

Solution structure of the PPIL1 bound to a fragment of SKIP

Authors

Wang, X., Wu, J., Shi, Y.

Assembly

PPIL1/SKIP

Entity

1. PPIL1/SKIP (polymer, Thiol state: all free), 203 monomers, 21510.04 Da Detail

MAAIPPDSWQ PPNVYLETSM GIIVLELYWK HAPKTCKNFA ELARRGYYNG TKFHRIIKDF MIQGGDPTGT GRGGASIYGK QFEDELHPDL KFTGAGILAM ANAGPDTNGS QFFVTLAPTQ WLDGKHTIFG RVCQGIGMVN RVGMVETNSQ DRPVDDVKII KAYPSGGGGS GGGSGGGSGG GSGDGGAFPE IHVAQYPLDM GRK

Formula weight

21510.04 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

CYANA and simulated annealin

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.6 %, Completeness: 77.8 %, Completeness (bb): 78.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	77.8 % (1752 of 2251)	85.2 % (995 of 1168)	64.3 % (563 of 875)	93.3 % (194 of 208)
Backbone	78.6 % (937 of 1192)	89.7 % (385 of 429)	65.6 % (376 of 573)	92.6 % (176 of 190)
Sidechain	79.4 % (973 of 1226)	82.5 % (610 of 739)	73.6 % (345 of 469)	100.0 % (18 of 18)
Aromatic	27.7 % (56 of 202)	45.5 % (46 of 101)	7.1 % (7 of 98)	100.0 % (3 of 3)
Methyl	99.5 % (181 of 182)	98.9 % (90 of 91)	100.0 % (91 of 91)

1. PPIL1/SKIP

Show sample condition

Sample

Solvent system 100% H2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 50mM phosphate buffer, 50 mM NaCl

#	Name	Isotope labeling	Concentration
1	D2O	natural abundance	100 %
2	entity_2	natural abundance
3	phosphate buffer	natural abundance	50 mM
4	NaCl	natural abundance	50 mM

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: -0.03 ppm, Outliers: 2 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: -0.03 ppm, Outliers: 2 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

Protein Blocks Logo

Calculated from 20 models in PDB: 2K7N, Strand ID: A Detail

Release date

2010-01-10

Citation

A large intrinsically disordered region in SKIP and its disorder-order transition induced by PPIL1 binding revealed by NMR
Wang, X., Zhang, S., Zhang, J., Huang, X., Xu, C., Wang, W., Liu, Z., Wu, J., Shi, Y.
J. Biol. Chem. (2010), 285, 4951-4963, PubMed 20007319 , DOI 10.1074/jbc.M109.087528 , Abstract

Related entities 1. PPIL1/SKIP, : 1 : 22 : 20 entities Detail

Interaction partners 1. PPIL1/SKIP, : 23 interactors Detail

More details for 23 interactors identified by 8 citations

Experiments performed 2 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15922_2k7n.nef
Input source #2: Coordindates	2k7n.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
MAAIPPDSWQPPNVYLETSMGIIVLELYWKHAPKTCKNFAELARRGYYNGTKFHRIIKDFMIQGGDPTGTGRGGASIYGKQFEDELHPDLKFTGAGILAM
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MAAIPPDSWQPPNVYLETSMGIIVLELYWKHAPKTCKNFAELARRGYYNGTKFHRIIKDFMIQGGDPTGTGRGGASIYGKQFEDELHPDLKFTGAGILAM

-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200
ANAGPDTNGSQFFVTLAPTQWLDGKHTIFGRVCQGIGMVNRVGMVETNSQDRPVDDVKIIKAYPSGGGGSGGGSGGGSGGGSGDGGAFPEIHVAQYPLDM
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ANAGPDTNGSQFFVTLAPTQWLDGKHTIFGRVCQGIGMVNRVGMVETNSQDRPVDDVKIIKAYPSGGGGSGGGSGGGSGGGSGDGGAFPEIHVAQYPLDM

---
GRK
|||
GRK

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	203	0	0	100.0

Content subtype: combined_15922_2k7n.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1689		90.1 (chain: A, length: 203)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	4048 (1)	noe	90.1 (chain: A, length: 203)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	110 (1)	hbond	33.0 (chain: A, length: 203)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	112 (112)	.	37.4 (chain: A, length: 203)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 203, Sequence coverage: 90.1%
- Total number of assignments
  - ¹H chemical shifts: 984
  - ¹³C chemical shifts: 519
  - ¹⁵N chemical shifts: 186
- 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)
115	THR	HG1	5.137

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1168	983	84.2
¹³C chemical shifts	875	519	59.3
¹⁵N chemical shifts	216	186	86.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	429	372	86.7
¹³C chemical shifts	406	182	44.8
¹⁵N chemical shifts	190	168	88.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	739	611	82.7
¹³C chemical shifts	469	337	71.9
¹⁵N chemical shifts	26	18	69.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	98	96	98.0
¹³C chemical shifts	98	96	98.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	101	41	40.6
¹³C chemical shifts	98	0	0.0
¹⁵N chemical shifts	3	3	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 203, Sequence coverage: 90.1%
- Total number of restraints: 4048
- Weight of restraints: 1.0 (4048)
- Potential type of restraints: square-well-parabolic (4048)
- Range of distance target values: 2.07, 3.92 (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: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 203, Sequence coverage: 33.0%
  - Total number of restraints: 110
  - Weight of restraints: 1.0 (110)
  - Potential type of restraints: square-well-parabolic (110)
  - Range of distance target values: 2.0, 3.05 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 203, Sequence coverage: 37.4%
- Total number of restraints: 112
- Total number of restraints per polymer type: 112
- Weight of restraints: 1.0 (112)
- Potential type of restraints: square-well-parabolic (112)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue

Keywords beta barrel, disorder-order transition, hook-like

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Found 1 Document (1.783 seconds)

BMRB: 15922

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. PPIL1/SKIP, : 1 : 22 : 20 entities Detail

Interaction partners 1. PPIL1/SKIP, : 23 interactors Detail

Experiments performed 2 experiments Detail

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail