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Found 1 Document (1.231 seconds)

BMRB: 16638

2KRG

Solution Structure of human sodium/ hydrogen exchange regulatory factor 1(150-358).

Authors

Bhattacharya, S., Dai, Z., Li, J., Baxter, S., Callaway, D.J. E., Cowburn, D., Bu, Z.

Assembly

NHERF1 (150-358)

Entity

1. NHERF1 (150-358) (polymer, Thiol state: all free), 216 monomers, 23636.16 Da Detail

GIDPFTMLRP RLCTMKKGPS GYGFNLHSDK SKPGQFIRSV DPDSPAEASG LRAQDRIVEV NGVCMEGKQH GDVVSAIRAG GDETKLLVVD RETDEFFKKC RVIPSQEHLN GPLPVPFTNG EIQKENSREA LAEAALESPR PALVRSASSD TSEELNSQDS PPKQDSTAPS STSSSDPILD FNISLAMAKE RAHQKRSSKR APQMDWSKKN ELFSNL

Formula weight

23636.16 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

torsion angle dynamics, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.4 %, Completeness: 84.4 %, Completeness (bb): 88.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	84.4 % (2062 of 2442)	84.9 % (1094 of 1288)	84.0 % (786 of 936)	83.5 % (182 of 218)
Backbone	88.9 % (1122 of 1262)	89.0 % (381 of 428)	89.6 % (569 of 635)	86.4 % (172 of 199)
Sidechain	81.6 % (1128 of 1383)	83.0 % (714 of 860)	80.2 % (404 of 504)	52.6 % (10 of 19)
Aromatic	54.3 % (63 of 116)	72.4 % (42 of 58)	35.1 % (20 of 57)	100.0 % (1 of 1)
Methyl	98.9 % (186 of 188)	98.9 % (93 of 94)	98.9 % (93 of 94)

1. NHERF1 (150-358)

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5

#	Name	Isotope labeling	Concentration
1	NHERF1 (150-358)	[U-100% 13C; U-100% 15N]	557 uM
2	HEPES	natural abundance	20 mM
3	sodium chloride	natural abundance	150 mM
4	DTT	natural abundance	0.5 mM
5	PMSF	natural abundance	0.1 mM
6	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5

#	Name	Isotope labeling	Concentration
7	NHERF1 (150-358)	[U-100% 13C; U-100% 15N; U-80% 2H]	389 uM
8	HEPES	natural abundance	20 mM
9	sodium chloride	natural abundance	150 mM
10	DTT	natural abundance	0.5 mM
11	PMSF	natural abundance	0.1 mM
12	D2O	natural abundance	10 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5, Details Selectively Labeled Sample.

#	Name	Isotope labeling	Concentration
13	NHERF1 (150-358)	[U-100% 13C; U-100% 15N]-Leu,Val,Phe	413 uM
14	HEPES	natural abundance	20 mM
15	sodium chloride	natural abundance	150 mM
16	DTT	natural abundance	0.5 mM
17	PMSF	natural abundance	0.1 mM
18	D2O	natural abundance	10 %

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: -0.1 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: -0.1 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: -0.04 ppm, Outliers: 2 Detail

LACS Plot; CO

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: -0.08 ppm, Outliers: 6 Detail

Protein Blocks Logo

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

Release date

2010-01-31

Citation

A conformational switch in the scaffolding protein NHERF1 controls autoinhibition and complex formation
Bhattacharya, S., Dai, Z., Li, J., Baxter, S., Callaway, D.J.E., Cowburn, D., Bu, Z.
J. Biol. Chem. (2010), 285, 9981-9994, PubMed 20042604 , DOI 10.1074/jbc.M109.074005 , Abstract

Related entities 1. NHERF1 (150-358), : 1 : 2 : 17 entities Detail

Interaction partners 1. NHERF1 (150-358), : 37 interactors Detail

More details for 37 interactors identified by 24 citations

Experiments performed 16 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 303 K, pH 7.5

#	Name	Isotope labeling	Concentration
1	NHERF1 (150-358)	[U-100% 13C; U-100% 15N]	557 uM
2	HEPES	natural abundance	20 mM
3	sodium chloride	natural abundance	150 mM
4	DTT	natural abundance	0.5 mM
5	PMSF	natural abundance	0.1 mM
6	D2O	natural abundance	10 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5

#	Name	Isotope labeling	Concentration
1	NHERF1 (150-358)	[U-100% 13C; U-100% 15N]	557 uM
2	HEPES	natural abundance	20 mM
3	sodium chloride	natural abundance	150 mM
4	DTT	natural abundance	0.5 mM
5	PMSF	natural abundance	0.1 mM
6	D2O	natural abundance	10 %

3 3D HNCACB

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5

#	Name	Isotope labeling	Concentration
1	NHERF1 (150-358)	[U-100% 13C; U-100% 15N]	557 uM
2	HEPES	natural abundance	20 mM
3	sodium chloride	natural abundance	150 mM
4	DTT	natural abundance	0.5 mM
5	PMSF	natural abundance	0.1 mM
6	D2O	natural abundance	10 %

4 3D CBCA(CO)NH

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5

#	Name	Isotope labeling	Concentration
1	NHERF1 (150-358)	[U-100% 13C; U-100% 15N]	557 uM
2	HEPES	natural abundance	20 mM
3	sodium chloride	natural abundance	150 mM
4	DTT	natural abundance	0.5 mM
5	PMSF	natural abundance	0.1 mM
6	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 303 K, pH 7.5

#	Name	Isotope labeling	Concentration
1	NHERF1 (150-358)	[U-100% 13C; U-100% 15N]	557 uM
2	HEPES	natural abundance	20 mM
3	sodium chloride	natural abundance	150 mM
4	DTT	natural abundance	0.5 mM
5	PMSF	natural abundance	0.1 mM
6	D2O	natural abundance	10 %

6 3D HN(CO)CA

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5

#	Name	Isotope labeling	Concentration
1	NHERF1 (150-358)	[U-100% 13C; U-100% 15N]	557 uM
2	HEPES	natural abundance	20 mM
3	sodium chloride	natural abundance	150 mM
4	DTT	natural abundance	0.5 mM
5	PMSF	natural abundance	0.1 mM
6	D2O	natural abundance	10 %

7 3D HNCO

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5

#	Name	Isotope labeling	Concentration
1	NHERF1 (150-358)	[U-100% 13C; U-100% 15N]	557 uM
2	HEPES	natural abundance	20 mM
3	sodium chloride	natural abundance	150 mM
4	DTT	natural abundance	0.5 mM
5	PMSF	natural abundance	0.1 mM
6	D2O	natural abundance	10 %

8 3D HNCACB

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5

#	Name	Isotope labeling	Concentration
7	NHERF1 (150-358)	[U-100% 13C; U-100% 15N; U-80% 2H]	389 uM
8	HEPES	natural abundance	20 mM
9	sodium chloride	natural abundance	150 mM
10	DTT	natural abundance	0.5 mM
11	PMSF	natural abundance	0.1 mM
12	D2O	natural abundance	10 %

9 3D HNCACB

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5, Details Selectively Labeled Sample.

#	Name	Isotope labeling	Concentration
13	NHERF1 (150-358)	[U-100% 13C; U-100% 15N]-Leu,Val,Phe	413 uM
14	HEPES	natural abundance	20 mM
15	sodium chloride	natural abundance	150 mM
16	DTT	natural abundance	0.5 mM
17	PMSF	natural abundance	0.1 mM
18	D2O	natural abundance	10 %

10 3D 1H-15N NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5

#	Name	Isotope labeling	Concentration
1	NHERF1 (150-358)	[U-100% 13C; U-100% 15N]	557 uM
2	HEPES	natural abundance	20 mM
3	sodium chloride	natural abundance	150 mM
4	DTT	natural abundance	0.5 mM
5	PMSF	natural abundance	0.1 mM
6	D2O	natural abundance	10 %

11 3D 1H-13C NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5

#	Name	Isotope labeling	Concentration
1	NHERF1 (150-358)	[U-100% 13C; U-100% 15N]	557 uM
2	HEPES	natural abundance	20 mM
3	sodium chloride	natural abundance	150 mM
4	DTT	natural abundance	0.5 mM
5	PMSF	natural abundance	0.1 mM
6	D2O	natural abundance	10 %

12 3D 1H-15N NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5, Details Selectively Labeled Sample.

#	Name	Isotope labeling	Concentration
13	NHERF1 (150-358)	[U-100% 13C; U-100% 15N]-Leu,Val,Phe	413 uM
14	HEPES	natural abundance	20 mM
15	sodium chloride	natural abundance	150 mM
16	DTT	natural abundance	0.5 mM
17	PMSF	natural abundance	0.1 mM
18	D2O	natural abundance	10 %

13 3D 1H-13C NOESY

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5, Details Selectively Labeled Sample.

#	Name	Isotope labeling	Concentration
13	NHERF1 (150-358)	[U-100% 13C; U-100% 15N]-Leu,Val,Phe	413 uM
14	HEPES	natural abundance	20 mM
15	sodium chloride	natural abundance	150 mM
16	DTT	natural abundance	0.5 mM
17	PMSF	natural abundance	0.1 mM
18	D2O	natural abundance	10 %

14 3D H(CCO)NH

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5

#	Name	Isotope labeling	Concentration
1	NHERF1 (150-358)	[U-100% 13C; U-100% 15N]	557 uM
2	HEPES	natural abundance	20 mM
3	sodium chloride	natural abundance	150 mM
4	DTT	natural abundance	0.5 mM
5	PMSF	natural abundance	0.1 mM
6	D2O	natural abundance	10 %

15 3D HCCH-TOCSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5

#	Name	Isotope labeling	Concentration
1	NHERF1 (150-358)	[U-100% 13C; U-100% 15N]	557 uM
2	HEPES	natural abundance	20 mM
3	sodium chloride	natural abundance	150 mM
4	DTT	natural abundance	0.5 mM
5	PMSF	natural abundance	0.1 mM
6	D2O	natural abundance	10 %

16 3D HCCH-COSY

Instrument

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.5

#	Name	Isotope labeling	Concentration
1	NHERF1 (150-358)	[U-100% 13C; U-100% 15N]	557 uM
2	HEPES	natural abundance	20 mM
3	sodium chloride	natural abundance	150 mM
4	DTT	natural abundance	0.5 mM
5	PMSF	natural abundance	0.1 mM
6	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_16638_2krg.nef
Input source #2: Coordindates	2krg.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

-----150-------160-------170-------180-------190-------200-------210-------220-------230-------240--
GIDPFTMLRPRLCTMKKGPSGYGFNLHSDKSKPGQFIRSVDPDSPAEASGLRAQDRIVEVNGVCMEGKQHGDVVSAIRAGGDETKLLVVDRETDEFFKKC
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GIDPFTMLRPRLCTMKKGPSGYGFNLHSDKSKPGQFIRSVDPDSPAEASGLRAQDRIVEVNGVCMEGKQHGDVVSAIRAGGDETKLLVVDRETDEFFKKC
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-----250-------260-------270-------280-------290-------300-------310-------320-------330-------340--
RVIPSQEHLNGPLPVPFTNGEIQKENSREALAEAALESPRPALVRSASSDTSEELNSQDSPPKQDSTAPSSTSSSDPILDFNISLAMAKERAHQKRSSKR
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
RVIPSQEHLNGPLPVPFTNGEIQKENSREALAEAALESPRPALVRSASSDTSEELNSQDSPPKQDSTAPSSTSSSDPILDFNISLAMAKERAHQKRSSKR
-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200

-----350--------
APQMDWSKKNELFSNL
||||||||||||||||
APQMDWSKKNELFSNL
-------210------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	216	0	0	100.0

Content subtype: combined_16638_2krg.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1987		91.7 (chain: A, length: 216)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	3796 (1)	noe	82.9 (chain: A, length: 216)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	141 (141)	.	43.5 (chain: A, length: 216)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 216, Sequence coverage: 91.7%
- Total number of assignments
  - ¹H chemical shifts: 1055
  - ¹³C chemical shifts: 758
  - ¹⁵N chemical shifts: 174
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
153	ARG	HH11	6.855
153	ARG	HH12	6.855
153	ARG	NH1	83.576
186	SER	HG	6.656
191	SER	HG	5.097
226	THR	HG1	4.163
235	THR	HG1	6.123

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1288	1049	81.4
¹³C chemical shifts	936	758	81.0
¹⁵N chemical shifts	232	173	74.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	428	367	85.7
¹³C chemical shifts	432	369	85.4
¹⁵N chemical shifts	199	164	82.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	860	682	79.3
¹³C chemical shifts	504	389	77.2
¹⁵N chemical shifts	33	9	27.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	99	93	93.9
¹³C chemical shifts	99	94	94.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	58	40	69.0
¹³C chemical shifts	57	20	35.1
¹⁵N chemical shifts	1	1	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: 216, Sequence coverage: 82.9%
- Total number of restraints: 3796
- Weight of restraints: 1.0 (3796)
- Potential type of restraints: square-well-parabolic (3796)
- Range of distance target values: 2.01, 3.9 (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: 216, Sequence coverage: 43.5%
- Total number of restraints: 141
- Total number of restraints per polymer type: 141
- Weight of restraints: 1.0 (141)
- Potential type of restraints: square-well-parabolic (141)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue

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Found 1 Document (1.231 seconds)

BMRB: 16638

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. NHERF1 (150-358), : 1 : 2 : 17 entities Detail

Interaction partners 1. NHERF1 (150-358), : 37 interactors Detail

Experiments performed 16 experiments Detail

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NMR combined restraints 4 contents Detail