BMRBj - BMREntryMaster

Found 1 Document (0.624 seconds)

BMRB: 30321

5WOE

Solution structure of the sorting nexin 25 phox-homology domain

Authors

Chin, Y.K.Y., Mas, C., Mobli, M., Collins, B.M.

Assembly

Sorting nexin-25

Entity

1. Sorting nexin-25 (polymer, Thiol state: all free), 125 monomers, 14229.18 Da Detail

GSNLGMWKAS ITSGEVTEEN GEQLPCYFVM VSLQEVGGVE TKNWTVPRRL SEFQNLHRKL SECVPSLKKV QLPSLSKLPF KSIDQKFMEK SKNQLNKFLQ NLLSDERLCQ SEALYAFLSP SPDYL

Formula weight

14229.18 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 95.4 %, Completeness (bb): 97.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	95.4 % (1447 of 1517)	96.2 % (769 of 799)	93.7 % (546 of 583)	97.8 % (132 of 135)
Backbone	97.4 % (717 of 736)	98.4 % (245 of 249)	97.0 % (358 of 369)	96.6 % (114 of 118)
Sidechain	92.2 % (830 of 900)	93.5 % (514 of 550)	90.1 % (300 of 333)	94.1 % (16 of 17)
Aromatic	79.5 % (89 of 112)	92.9 % (52 of 56)	64.8 % (35 of 54)	100.0 % (2 of 2)
Methyl	100.0 % (126 of 126)	100.0 % (63 of 63)	100.0 % (63 of 63)

1. entity 1

GSNLGMWKAS ITSGEVTEEN GEQLPCYFVM VSLQEVGGVE TKNWTVPRRL SEFQNLHRKL SECVPSLKKV QLPSLSKLPF KSIDQKFMEK SKNQLNKFLQ NLLSDERLCQ SEALYAFLSP SPDYL

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.8 mM [U-99% 13C; U-99% 15N] SNX25, 20 mM HEPES, 100 mM NaCl, 2 mM DTT, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	2 mM
2	HEPES	natural abundance	20 mM
3	NaCl	natural abundance	100 mM
4	SNX25	[U-99% 13C; U-99% 15N]	0.8 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.78 ppm	internal	indirect	0.2514495
¹H	water	protons	4.78 ppm	internal	direct	1.0
¹⁵N	water	protons	4.78 ppm	internal	indirect	0.1013291

Referencing offset: -0.02 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.78 ppm	internal	indirect	0.2514495
¹H	water	protons	4.78 ppm	internal	direct	1.0
¹⁵N	water	protons	4.78 ppm	internal	indirect	0.1013291

Referencing offset: -0.02 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.78 ppm	internal	indirect	0.2514495
¹H	water	protons	4.78 ppm	internal	direct	1.0
¹⁵N	water	protons	4.78 ppm	internal	indirect	0.1013291

Referencing offset: -0.03 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.78 ppm	internal	indirect	0.2514495
¹H	water	protons	4.78 ppm	internal	direct	1.0
¹⁵N	water	protons	4.78 ppm	internal	indirect	0.1013291

Referencing offset: 0.02 ppm, Outliers: 1 Detail

Release date

2017-08-03

Citation

Classification of the human phox homology (PX) domains based on their phosphoinositide binding specificities
Chandra, M., Chin, Y.K., Mas, C., Feathers, J.R., Paul, B., Datta, S., Chen, K.E., Jia, X., Yang, Z., Norwood, S.J., Mohanty, B., Bugarcic, A., Teasdale, R.D., Henne, W.M., Mobli, M., Collins, B.M.
Nat. Commun. (2019), 10, 1528-1528, PubMed 30948714 , DOI 10.1038/s41467-019-09355-y , Abstract

Related entities 1. Sorting nexin-25, : 1 : 2 : 60 entities Detail

Interaction partners 1. Sorting nexin-25, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 8 experiments Detail

1 3D HNCO

Instrument

Bruker AvanceII - 900 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 0.8 mM [U-99% 13C; U-99% 15N] SNX25, 20 mM HEPES, 100 mM NaCl, 2 mM DTT, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	2 mM
2	HEPES	natural abundance	20 mM
3	NaCl	natural abundance	100 mM
4	SNX25	[U-99% 13C; U-99% 15N]	0.8 mM

2 3D CBCA(CO)NH

Instrument

Bruker AvanceII - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	2 mM
2	HEPES	natural abundance	20 mM
3	NaCl	natural abundance	100 mM
4	SNX25	[U-99% 13C; U-99% 15N]	0.8 mM

3 3D HNCACB

Instrument

Bruker AvanceII - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	2 mM
2	HEPES	natural abundance	20 mM
3	NaCl	natural abundance	100 mM
4	SNX25	[U-99% 13C; U-99% 15N]	0.8 mM

4 3D HBHA(CO)NH

Instrument

Bruker AvanceII - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	2 mM
2	HEPES	natural abundance	20 mM
3	NaCl	natural abundance	100 mM
4	SNX25	[U-99% 13C; U-99% 15N]	0.8 mM

5 2D 1H-15N HSQC

Instrument

Bruker AvanceII - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	2 mM
2	HEPES	natural abundance	20 mM
3	NaCl	natural abundance	100 mM
4	SNX25	[U-99% 13C; U-99% 15N]	0.8 mM

6 3D 1H-15N NOESY

Instrument

Bruker AvanceII - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	2 mM
2	HEPES	natural abundance	20 mM
3	NaCl	natural abundance	100 mM
4	SNX25	[U-99% 13C; U-99% 15N]	0.8 mM

7 3D 1H-13C NOESY aromatic

Instrument

Bruker AvanceII - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	2 mM
2	HEPES	natural abundance	20 mM
3	NaCl	natural abundance	100 mM
4	SNX25	[U-99% 13C; U-99% 15N]	0.8 mM

8 3D 1H-13C NOESY aliphatic

Instrument

Bruker AvanceII - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DTT	natural abundance	2 mM
2	HEPES	natural abundance	20 mM
3	NaCl	natural abundance	100 mM
4	SNX25	[U-99% 13C; U-99% 15N]	0.8 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30321_5woe.nef
Input source #2: Coordindates	5woe.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

--670-------680-------690-------700-------710-------720-------730-------740-------750-------760-----
GSNLGMWKASITSGEVTEENGEQLPCYFVMVSLQEVGGVETKNWTVPRRLSEFQNLHRKLSECVPSLKKVQLPSLSKLPFKSIDQKFMEKSKNQLNKFLQ
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSNLGMWKASITSGEVTEENGEQLPCYFVMVSLQEVGGVETKNWTVPRRLSEFQNLHRKLSECVPSLKKVQLPSLSKLPFKSIDQKFMEKSKNQLNKFLQ
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

--770-------780-------790
NLLSDERLCQSEALYAFLSPSPDYL
|||||||||||||||||||||||||
NLLSDERLCQSEALYAFLSPSPDYL
-------110-------120-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	125	0	0	100.0

Content subtype: combined_30321_5woe.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1420		99.2 (chain: A, length: 125)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	4069 (1)	noe	99.2 (chain: A, length: 125)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	262 (262)	.	96.8 (chain: A, length: 125)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 125, Sequence coverage: 99.2%
- Total number of assignments
  - ¹H chemical shifts: 754
  - ¹³C chemical shifts: 535
  - ¹⁵N chemical shifts: 131
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	799	754	94.4
¹³C chemical shifts	583	535	91.8
¹⁵N chemical shifts	139	131	94.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	249	243	97.6
¹³C chemical shifts	250	238	95.2
¹⁵N chemical shifts	118	115	97.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	550	511	92.9
¹³C chemical shifts	333	297	89.2
¹⁵N chemical shifts	21	16	76.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	66	66	100.0
¹³C chemical shifts	66	66	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	56	51	91.1
¹³C chemical shifts	54	32	59.3
¹⁵N chemical shifts	2	2	100.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 125, Sequence coverage: 99.2%
- Total number of restraints: 4069
- Weight of restraints: 1.0 (4069)
- Potential type of restraints: upper-bound-parabolic (4069)
- Range of distance target values: 2.34, 5.5 (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: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 125, Sequence coverage: 96.8%
- Total number of restraints: 262
- Total number of restraints per polymer type: 262
- Weight of restraints: 1.0 (262)
- Potential type of restraints: square-well-parabolic (262)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Mdm1, PX domain, PXA domain, PXC domain, RGS domain, SNX, SNX13, SNX14, SNX19, SNX25, endosome, sorting nexin

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Found 1 Document (0.624 seconds)

BMRB: 30321

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Sorting nexin-25, : 1 : 2 : 60 entities Detail

Interaction partners 1. Sorting nexin-25, : 1 interactors Detail

Experiments performed 8 experiments Detail

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NMR combined restraints 4 contents Detail