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BMRB: 15370

2JSN

solution structure of the atypical PDZ-like domain of synbindin

Authors

Feng, Y., Fan, S., Gong, W., Xia, B.

Assembly

apd monomer

Entity

1. apd monomer (polymer, Thiol state: not present), 96 monomers, 10801.05 Da Detail

MGHHHHHHLD SYAPRAEAEK TFSYPLDLLL KLHDERVLVA FGQRDGIRVG HAVLAINGMD VNGRYTADGK EVLEYLGNPA NYPVSIRFGR PRLTSN

Formula weight

10801.05 Da

Source organism

Exptl. method

Refine. method

molecular dynamics, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 87.5 %, Completeness: 76.4 %, Completeness (bb): 81.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	76.4 % (841 of 1101)	75.3 % (429 of 570)	76.7 % (333 of 434)	81.4 % (79 of 97)
Backbone	81.8 % (463 of 566)	81.1 % (159 of 196)	82.8 % (231 of 279)	80.2 % (73 of 91)
Sidechain	73.0 % (454 of 622)	72.2 % (270 of 374)	73.6 % (178 of 242)	100.0 % (6 of 6)
Aromatic	62.7 % (64 of 102)	64.7 % (33 of 51)	60.8 % (31 of 51)
Methyl	75.5 % (80 of 106)	73.6 % (39 of 53)	77.4 % (41 of 53)

1. apd

MGHHHHHHLD SYAPRAEAEK TFSYPLDLLL KLHDERVLVA FGQRDGIRVG HAVLAINGMD VNGRYTADGK EVLEYLGNPA NYPVSIRFGR PRLTSN

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	apd	[U-13C; U-15N]		1.0 ~ 1.5 (±0.1) mM
2	potassium phosphate	natural abundance		50 (±1.0) mM
3	DSS	natural abundance		0.01 %
4	sodium azide	natural abundance		0.01 %

LACS Plot; CA

Referencing offset: -0.08 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: -0.08 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: -0.04 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.25 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2009-04-23

Citation

Solution structure of synbindin atypical PDZ domain and interaction with syndecan-2
Fan, S., Feng, Y., Wei, Z., Xia, B., Gong, W.
Protein Pept. Lett. (2009), 16, 189-195, PubMed 19200043 , DOI: , Abstract

Related entities 1. apd monomer, : 1 : 12 entities Detail

Interaction partners 1. apd monomer, : 15 interactors Detail

More details for 15 interactors identified by 9 citations

Experiments performed 15 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	apd	[U-13C; U-15N]		1.0 ~ 1.5 (±0.1) mM
2	potassium phosphate	natural abundance		50 (±1.0) mM
3	DSS	natural abundance		0.01 %
4	sodium azide	natural abundance		0.01 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	apd	[U-13C; U-15N]		1.0 ~ 1.5 (±0.1) mM
2	potassium phosphate	natural abundance		50 (±1.0) mM
3	DSS	natural abundance		0.01 %
4	sodium azide	natural abundance		0.01 %

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	apd	[U-13C; U-15N]		1.0 ~ 1.5 (±0.1) mM
2	potassium phosphate	natural abundance		50 (±1.0) mM
3	DSS	natural abundance		0.01 %
4	sodium azide	natural abundance		0.01 %

4 3D HNCACB

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	apd	[U-13C; U-15N]		1.0 ~ 1.5 (±0.1) mM
2	potassium phosphate	natural abundance		50 (±1.0) mM
3	DSS	natural abundance		0.01 %
4	sodium azide	natural abundance		0.01 %

5 3D HNCA

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	apd	[U-13C; U-15N]		1.0 ~ 1.5 (±0.1) mM
2	potassium phosphate	natural abundance		50 (±1.0) mM
3	DSS	natural abundance		0.01 %
4	sodium azide	natural abundance		0.01 %

6 3D HNCO

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	apd	[U-13C; U-15N]		1.0 ~ 1.5 (±0.1) mM
2	potassium phosphate	natural abundance		50 (±1.0) mM
3	DSS	natural abundance		0.01 %
4	sodium azide	natural abundance		0.01 %

7 3D HCCH-TOCSY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	apd	[U-13C; U-15N]		1.0 ~ 1.5 (±0.1) mM
2	potassium phosphate	natural abundance		50 (±1.0) mM
3	DSS	natural abundance		0.01 %
4	sodium azide	natural abundance		0.01 %

8 3D HBHA(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	apd	[U-13C; U-15N]		1.0 ~ 1.5 (±0.1) mM
2	potassium phosphate	natural abundance		50 (±1.0) mM
3	DSS	natural abundance		0.01 %
4	sodium azide	natural abundance		0.01 %

9 2D CB(CGCD)HD

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	apd	[U-13C; U-15N]		1.0 ~ 1.5 (±0.1) mM
2	potassium phosphate	natural abundance		50 (±1.0) mM
3	DSS	natural abundance		0.01 %
4	sodium azide	natural abundance		0.01 %

10 3D HN(CA)CO

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	apd	[U-13C; U-15N]		1.0 ~ 1.5 (±0.1) mM
2	potassium phosphate	natural abundance		50 (±1.0) mM
3	DSS	natural abundance		0.01 %
4	sodium azide	natural abundance		0.01 %

11 3D 1H-15N TOCSY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	apd	[U-13C; U-15N]		1.0 ~ 1.5 (±0.1) mM
2	potassium phosphate	natural abundance		50 (±1.0) mM
3	DSS	natural abundance		0.01 %
4	sodium azide	natural abundance		0.01 %

12 3D 1H-15N NOESY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	apd	[U-13C; U-15N]		1.0 ~ 1.5 (±0.1) mM
2	potassium phosphate	natural abundance		50 (±1.0) mM
3	DSS	natural abundance		0.01 %
4	sodium azide	natural abundance		0.01 %

13 3D 1H-13C NOESY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	apd	[U-13C; U-15N]		1.0 ~ 1.5 (±0.1) mM
2	potassium phosphate	natural abundance		50 (±1.0) mM
3	DSS	natural abundance		0.01 %
4	sodium azide	natural abundance		0.01 %

14 3D HCCH-COSY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	apd	[U-13C; U-15N]		1.0 ~ 1.5 (±0.1) mM
2	potassium phosphate	natural abundance		50 (±1.0) mM
3	DSS	natural abundance		0.01 %
4	sodium azide	natural abundance		0.01 %

15 3D CCH-TOCSY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	apd	[U-13C; U-15N]		1.0 ~ 1.5 (±0.1) mM
2	potassium phosphate	natural abundance		50 (±1.0) mM
3	DSS	natural abundance		0.01 %
4	sodium azide	natural abundance		0.01 %

NMR combined restraints 8 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15370_2jsn.nef
Input source #2: Coordindates	2jsn.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------
MGHHHHHHLDSYAPRAEAEKTFSYPLDLLLKLHDERVLVAFGQRDGIRVGHAVLAINGMDVNGRYTADGKEVLEYLGNPANYPVSIRFGRPRLTSN
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGHHHHHHLDSYAPRAEAEKTFSYPLDLLLKLHDERVLVAFGQRDGIRVGHAVLAINGMDVNGRYTADGKEVLEYLGNPANYPVSIRFGRPRLTSN

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	96	0	0	100.0

Content subtype: combined_15370_2jsn.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	829		85.4 (chain: A, length: 96)
1	Distance restraints	AMBER_distance_constraints_6	Warning	6484 (1)	noe	85.4 (chain: A, length: 96)
2	Distance restraints	AMBER_distance_constraints_11	Warning	6484 (1)	noe	85.4 (chain: A, length: 96)
3	Distance restraints	AMBER_distance_constraints_5	Warning	40 (1)	hbond	26.0 (chain: A, length: 96)
4	Distance restraints	AMBER_distance_constraints_10	Warning	40 (1)	hbond	26.0 (chain: A, length: 96)
1	Dihedral angle restraints	AMBER_dihedral_4	OK	64 (64)	.	57.3 (chain: A, length: 96)
2	Dihedral angle restraints	AMBER_dihedral_9	OK	64 (64)	.	57.3 (chain: A, length: 96)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 85.4%
- Total number of assignments
  - ¹H chemical shifts: 425
  - ¹³C chemical shifts: 328
  - ¹⁵N chemical shifts: 76
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- Tautomeric state of HIS
- 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: AMBER_distance_constraints_6
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 85.4%
- Total number of restraints: 6243
- Weight of restraints: 1.0 (6243)
- Potential type of restraints: square-well-parabolic (6243)
- Range of distance target values: 2.4, 7.82 (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: AMBER_distance_constraints_11
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 85.4%
  - Total number of restraints: 6243
  - Weight of restraints: 1.0 (6243)
  - Potential type of restraints: square-well-parabolic (6243)
  - Range of distance target values: 2.4, 7.82 (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: AMBER_distance_constraints_5
    - Status: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 26.0%
    - Total number of restraints: 40
    - Weight of restraints: 1.0 (40)
    - Potential type of restraints: square-well-parabolic (40)
    - Range of distance target values: 2.15, 2.65 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map
    - Saveframe: AMBER_distance_constraints_10
      - Status: Warning
      - Experiment type: hbond
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 26.0%
      - Total number of restraints: 40
        Total hydrogen bond restraints: 40
        O...H-x: 9
        O...h-N: 9
        Long range: 22
        O...H-x: 11
        O...h-N: 11
      - Weight of restraints: 1.0 (40)
        Total hydrogen bond restraints: 1.0 (40)
        O...H-x: 1.0 (9)
        O...h-N: 1.0 (9)
        Long range: 1.0 (22)
        O...H-x: 1.0 (11)
        O...h-N: 1.0 (11)
      - Potential type of restraints: square-well-parabolic (40)
        Total hydrogen bond restraints: square-well-parabolic (40)
        O...H-x: square-well-parabolic (9)
        O...h-N: square-well-parabolic (9)
        Long range: square-well-parabolic (22)
        O...H-x: square-well-parabolic (11)
        O...h-N: square-well-parabolic (11)
      - Range of distance target values: 2.15, 2.65 (Å)
      - Histogram of distance target values
      - Distance restraints per residue
        Chain_ID: A
      - Distance restraints on contact map

Dihedral angle restraints

Saveframe: AMBER_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 57.3%
- Total number of restraints: 64
- Total number of restraints per polymer type: 64
- Weight of restraints: 1.0 (64)
- Potential type of restraints: square-well-parabolic (64)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
- Saveframe: AMBER_dihedral_9
  - Status: OK
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 57.3%
  - Total number of restraints: 64
  - Total number of restraints per polymer type: 64
  - Weight of restraints: 1.0 (64)
  - Potential type of restraints: square-well-parabolic (64)
  - Plot of Phi-Psi angle restraints
  - Dihedral angle restraints per residue
    - Chain_ID: A

Keywords Protein Interaction