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BMRB: 18824

2M0T

Structural characterization of the extended PDZ1 domain from NHERF1.

Authors

Bhattacharya, S., Ju, J.H., Cowburn, D., Bu, Z.

Assembly

extended PDZ1 domain from NHERF1

Entity

1. extended PDZ1 domain from NHERF1 (polymer, Thiol state: all free), 117 monomers, 12805.47 Da Detail

GIDPFTMLPR LCCLEKGPNG YGFHLHGEKG KLGQYIRLVE PGSPAEKAGL LAGDRLVEVN GENVEKETHQ QVVSRIRAAL NAVRLLVVDP ETDEQLQKLG VQVREELLRA QEAPGQA

Formula weight

12805.47 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.1 %, Completeness: 94.5 %, Completeness (bb): 94.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	94.5 % (1267 of 1341)	95.0 % (669 of 704)	93.6 % (482 of 515)	95.1 % (116 of 122)
Backbone	94.6 % (651 of 688)	97.5 % (234 of 240)	92.6 % (313 of 338)	94.5 % (104 of 110)
Sidechain	94.7 % (717 of 757)	93.8 % (435 of 464)	96.1 % (270 of 281)	100.0 % (12 of 12)
Aromatic	89.6 % (43 of 48)	91.7 % (22 of 24)	87.5 % (21 of 24)
Methyl	100.0 % (144 of 144)	100.0 % (72 of 72)	100.0 % (72 of 72)

1. PDZ1

GIDPFTMLPR LCCLEKGPNG YGFHLHGEKG KLGQYIRLVE PGSPAEKAGL LAGDRLVEVN GENVEKETHQ QVVSRIRAAL NAVRLLVVDP ETDEQLQKLG VQVREELLRA QEAPGQA

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	PDZ1	[U-99% 13C; U-99% 15N]		400 uM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		150 mM
4	DTT	natural abundance		0.5 mM
5	EDTA	natural abundance		0.5 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: -0.01 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: -0.01 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: 0.09 ppm, Outliers: 3 Detail

LACS Plot; CO

Referencing offset: 0.12 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2M0T, Strand ID: A Detail

Release date

2013-04-21

Citation

Ligand-induced dynamic changes in extended PDZ domains from NHERF1
Bhattacharya, S., Ju, J., Orlova, N., Khajeh, J., Cowburn, D., Bu, Z.
J. Mol. Biol. (2013), 425, 2509-2528, PubMed 23583913 , DOI 10.1016/j.jmb.2013.04.001 , Abstract

Related entities 1. extended PDZ1 domain from NHERF1, : 1 : 1 : 3 : 118 entities Detail

Interaction partners 1. extended PDZ1 domain from NHERF1, : 38 interactors Detail

More details for 38 interactors identified by 22 citations

Experiments performed 14 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	PDZ1	[U-99% 13C; U-99% 15N]		400 uM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		150 mM
4	DTT	natural abundance		0.5 mM
5	EDTA	natural abundance		0.5 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

2 3D HNCACB

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	PDZ1	[U-99% 13C; U-99% 15N]		400 uM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		150 mM
4	DTT	natural abundance		0.5 mM
5	EDTA	natural abundance		0.5 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	PDZ1	[U-99% 13C; U-99% 15N]		400 uM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		150 mM
4	DTT	natural abundance		0.5 mM
5	EDTA	natural abundance		0.5 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

4 3D HNCO

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	PDZ1	[U-99% 13C; U-99% 15N]		400 uM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		150 mM
4	DTT	natural abundance		0.5 mM
5	EDTA	natural abundance		0.5 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

5 3D HNCA

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	PDZ1	[U-99% 13C; U-99% 15N]		400 uM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		150 mM
4	DTT	natural abundance		0.5 mM
5	EDTA	natural abundance		0.5 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

6 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	PDZ1	[U-99% 13C; U-99% 15N]		400 uM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		150 mM
4	DTT	natural abundance		0.5 mM
5	EDTA	natural abundance		0.5 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

7 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	PDZ1	[U-99% 13C; U-99% 15N]		400 uM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		150 mM
4	DTT	natural abundance		0.5 mM
5	EDTA	natural abundance		0.5 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

8 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	PDZ1	[U-99% 13C; U-99% 15N]		400 uM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		150 mM
4	DTT	natural abundance		0.5 mM
5	EDTA	natural abundance		0.5 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

9 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	PDZ1	[U-99% 13C; U-99% 15N]		400 uM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		150 mM
4	DTT	natural abundance		0.5 mM
5	EDTA	natural abundance		0.5 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

10 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	PDZ1	[U-99% 13C; U-99% 15N]		400 uM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		150 mM
4	DTT	natural abundance		0.5 mM
5	EDTA	natural abundance		0.5 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

11 3D H(CCO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	PDZ1	[U-99% 13C; U-99% 15N]		400 uM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		150 mM
4	DTT	natural abundance		0.5 mM
5	EDTA	natural abundance		0.5 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

12 3D HBHA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	PDZ1	[U-99% 13C; U-99% 15N]		400 uM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		150 mM
4	DTT	natural abundance		0.5 mM
5	EDTA	natural abundance		0.5 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

13 3D HCCH-COSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	PDZ1	[U-99% 13C; U-99% 15N]		400 uM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		150 mM
4	DTT	natural abundance		0.5 mM
5	EDTA	natural abundance		0.5 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

14 3D HCCH-TOCSY

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 288 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	PDZ1	[U-99% 13C; U-99% 15N]		400 uM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		150 mM
4	DTT	natural abundance		0.5 mM
5	EDTA	natural abundance		0.5 mM
6	H2O	natural abundance		90 %
7	D2O	natural abundance		10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18824_2m0t.nef
Input source #2: Coordindates	2m0t.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---
GIDPFTMLPRLCCLEKGPNGYGFHLHGEKGKLGQYIRLVEPGSPAEKAGLLAGDRLVEVNGENVEKETHQQVVSRIRAALNAVRLLVVDPETDEQLQKLG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GIDPFTMLPRLCCLEKGPNGYGFHLHGEKGKLGQYIRLVEPGSPAEKAGLLAGDRLVEVNGENVEKETHQQVVSRIRAALNAVRLLVVDPETDEQLQKLG
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

----110-------120
VQVREELLRAQEAPGQA
|||||||||||||||||
VQVREELLRAQEAPGQA
-------110-------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	117	0	0	100.0

Content subtype: combined_18824_2m0t.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1277		99.1 (chain: A, length: 117)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	3398 (1)	noe	98.3 (chain: A, length: 117)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	112 (112)	.	65.0 (chain: A, length: 117)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 117, Sequence coverage: 99.1%

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

----110-------120
VQVREELLRAQEAPGQA
||||| |||||||||||
VQVRE.LLRAQEAPGQA

Total number of assignments
- ¹H chemical shifts: 679
- ¹³C chemical shifts: 479
- ¹⁵N chemical shifts: 119

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
40	ARG	HH11	6.299
40	ARG	HH12	6.299
40	ARG	HH21	6.591
40	ARG	HH22	6.591
46	SER	HG	6.48
71	THR	HG1	5.51
78	ARG	HH11	6.664
78	ARG	HH21	6.727
80	ARG	HH11	6.383
80	ARG	HH12	6.383
80	ARG	HH21	6.745
80	ARG	HH22	6.745
112	ARG	HH11	6.437
112	ARG	HH12	6.437
112	ARG	HH21	6.68
112	ARG	HH22	6.68

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	704	663	94.2
¹³C chemical shifts	515	479	93.0
¹⁵N chemical shifts	130	119	91.5

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	240	234	97.5
¹³C chemical shifts	234	211	90.2
¹⁵N chemical shifts	110	103	93.6

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	464	429	92.5
¹³C chemical shifts	281	268	95.4
¹⁵N chemical shifts	20	16	80.0

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	73	72	98.6
¹³C chemical shifts	73	72	98.6

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	24	22	91.7
¹³C chemical shifts	24	21	87.5

Redox state of CYS
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: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 117, Sequence coverage: 98.3%
- Total number of restraints: 3398
- Weight of restraints: 1.0 (3398)
- Potential type of restraints: square-well-parabolic (3398)
- Range of distance target values: 2.07, 3.75 (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

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 117, Sequence coverage: 65.0%
- 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
  - Chain_ID: A

Keywords PDZ domain, Protein/Peptide