BMRBj - BMREntryMaster

Found 1 Document (1.467 seconds)

BMRB: 16119

2KDO

Structure of the human Shwachman-Bodian-Diamond syndrome protein, SBDS

Authors

de Oliveira, J.F., Sforca, M.L., Blumenschein, T., Guimaraes, B.G., Zanchin, N.IT., Zeri, A.M.

Assembly

SBDS

Entity

1. SBDS (polymer, Thiol state: all free), 252 monomers, 28957.34 Da Detail

GHMSIFTPTN QIRLTNVAVV RMKRAGKRFE IACYKNKVVG WRSGVEKDLD EVLQTHSVFV NVSKGQVAKK EDLISAFGTD DQTEICKQIL TKGEVQVSDK ERHTQLEQMF RDIATIVADK CVNPETKRPY TVILIERAMK DIHYSVKTNK STKQQALEVI KQLKEKMKIE RAHMRLRFIL PVNEGKKLKE KLKPLIKVIE SEDYGQQLEI VCLIDPGCFR EIDELIKKET KGKGSLEVLN LKDVEEGDEK FE

Formula weight

28957.34 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

DGSA-distance geometry simulated annealing, torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.4 %, Completeness: 79.3 %, Completeness (bb): 91.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	79.3 % (2435 of 3069)	73.3 % (1187 of 1619)	86.5 % (1022 of 1182)	84.3 % (226 of 268)
Backbone	91.7 % (1375 of 1500)	90.6 % (463 of 511)	93.1 % (692 of 743)	89.4 % (220 of 246)
Sidechain	71.0 % (1283 of 1808)	65.3 % (724 of 1108)	81.6 % (553 of 678)	27.3 % (6 of 22)
Aromatic	27.8 % (40 of 144)	38.9 % (28 of 72)	15.5 % (11 of 71)	100.0 % (1 of 1)
Methyl	88.0 % (264 of 300)	88.0 % (132 of 150)	88.0 % (132 of 150)

1. SBDS

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.2, Details sodium phosphate buffer

#	Name	Isotope labeling	Concentration
1	SBDS	[U-100% 13C; U-100% 15N; U-80% 2H]	0.5 mM
2	DTT	no	1.0 mM
3	sodium phosphate	no	50 mM
4	sodium chloride	no	20 mM
5	sodium azide	no	0.05 %
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.2, Details sodium phosphate buffer

#	Name	Isotope labeling	Concentration
8	SBDS	[U-99% 13C; U-99% 15N]	0.5 mM
9	DTT	no	1.0 mM
10	sodium phosphate	no	50 mM
11	sodium chloride	no	20 mM
12	sodium azide	no	0.05 %
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 7.2, Details sample_2 was liophilized and resuspended in 100% D2O.

#	Name	Isotope labeling	Concentration
15	SBDS	[U-99% 13C; U-99% 15N]	0.5 mM
16	DTT	no	1.0 mM
17	sodium phosphate	no	50 mM
18	sodium chloride	no	20 mM
19	sodium azide	no	0.05 %
20	D2O	natural abundance	100 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	ubiquitin	methyl carbons	43.0 ppm	external	indirect	1.0
¹H	water	protons	4.87 ppm	na	direct	1.0
¹⁵N	ubiquitin	nitrogen	119.0 ppm	external	indirect	1.0

Referencing offset: 1.37 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	ubiquitin	methyl carbons	43.0 ppm	external	indirect	1.0
¹H	water	protons	4.87 ppm	na	direct	1.0
¹⁵N	ubiquitin	nitrogen	119.0 ppm	external	indirect	1.0

Referencing offset: 1.37 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	ubiquitin	methyl carbons	43.0 ppm	external	indirect	1.0
¹H	water	protons	4.87 ppm	na	direct	1.0
¹⁵N	ubiquitin	nitrogen	119.0 ppm	external	indirect	1.0

Referencing offset: -0.07 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	ubiquitin	methyl carbons	43.0 ppm	external	indirect	1.0
¹H	water	protons	4.87 ppm	na	direct	1.0
¹⁵N	ubiquitin	nitrogen	119.0 ppm	external	indirect	1.0

Referencing offset: 2.72 ppm, Outliers: 4 Detail

Protein Blocks Logo

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

Release date

2010-01-10

Citation

Structure, dynamics, and RNA interaction analysis of the human SBDS protein
de Oliveira, J., Sforca, M.L., Blumenschein, T.M.A., Goldfeder, M.B., Guimaraes, B.G., Oliveira, C., Zanchin, N.I.T., Zeri, A.
J. Mol. Biol. (2010), 396, 1053-1069, PubMed 20053358 , DOI 10.1016/j.jmb.2009.12.039 , Abstract

Entries sharing articles Swiss-Prot: 1 entries Detail

Swiss-Prot: Q9Y3A5 released on 2000-05-30
Title SBDS_HUMAN Entity Ribosome maturation protein SBDS

Related entities 1. SBDS, : 1 : 10 : 28 entities Detail

Interaction partners 1. SBDS, : 10 interactors Detail

More details for 10 interactors identified by 5 citations

Experiments performed 15 experiments Detail

1 3D HNCACB

Instrument

Varian INOVA - 600 MHz with cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.2, Details sodium phosphate buffer

#	Name	Isotope labeling	Concentration
1	SBDS	[U-100% 13C; U-100% 15N; U-80% 2H]	0.5 mM
2	DTT	no	1.0 mM
3	sodium phosphate	no	50 mM
4	sodium chloride	no	20 mM
5	sodium azide	no	0.05 %
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

2 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz with cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.2, Details sodium phosphate buffer

#	Name	Isotope labeling	Concentration
1	SBDS	[U-100% 13C; U-100% 15N; U-80% 2H]	0.5 mM
2	DTT	no	1.0 mM
3	sodium phosphate	no	50 mM
4	sodium chloride	no	20 mM
5	sodium azide	no	0.05 %
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

3 3D HNCA

Instrument

Varian INOVA - 600 MHz with cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.2, Details sodium phosphate buffer

#	Name	Isotope labeling	Concentration
1	SBDS	[U-100% 13C; U-100% 15N; U-80% 2H]	0.5 mM
2	DTT	no	1.0 mM
3	sodium phosphate	no	50 mM
4	sodium chloride	no	20 mM
5	sodium azide	no	0.05 %
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

4 3D HN(CO)CA

Instrument

Varian INOVA - 600 MHz with cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.2, Details sodium phosphate buffer

#	Name	Isotope labeling	Concentration
1	SBDS	[U-100% 13C; U-100% 15N; U-80% 2H]	0.5 mM
2	DTT	no	1.0 mM
3	sodium phosphate	no	50 mM
4	sodium chloride	no	20 mM
5	sodium azide	no	0.05 %
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

5 3D HNCO

Instrument

Varian INOVA - 600 MHz with cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.2, Details sodium phosphate buffer

#	Name	Isotope labeling	Concentration
1	SBDS	[U-100% 13C; U-100% 15N; U-80% 2H]	0.5 mM
2	DTT	no	1.0 mM
3	sodium phosphate	no	50 mM
4	sodium chloride	no	20 mM
5	sodium azide	no	0.05 %
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

6 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz with cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.2, Details sodium phosphate buffer

#	Name	Isotope labeling	Concentration
8	SBDS	[U-99% 13C; U-99% 15N]	0.5 mM
9	DTT	no	1.0 mM
10	sodium phosphate	no	50 mM
11	sodium chloride	no	20 mM
12	sodium azide	no	0.05 %
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

7 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz with cryogenic probe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 7.2, Details sample_2 was liophilized and resuspended in 100% D2O.

#	Name	Isotope labeling	Concentration
15	SBDS	[U-99% 13C; U-99% 15N]	0.5 mM
16	DTT	no	1.0 mM
17	sodium phosphate	no	50 mM
18	sodium chloride	no	20 mM
19	sodium azide	no	0.05 %
20	D2O	natural abundance	100 %

8 3D 1H-13C NOESY

Instrument

Varian INOVA - 600 MHz with cryogenic probe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 7.2, Details sample_2 was liophilized and resuspended in 100% D2O.

#	Name	Isotope labeling	Concentration
15	SBDS	[U-99% 13C; U-99% 15N]	0.5 mM
16	DTT	no	1.0 mM
17	sodium phosphate	no	50 mM
18	sodium chloride	no	20 mM
19	sodium azide	no	0.05 %
20	D2O	natural abundance	100 %

9 3D 1H-15N TOCSY

Instrument

Varian INOVA - 600 MHz with cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.2, Details sodium phosphate buffer

#	Name	Isotope labeling	Concentration
8	SBDS	[U-99% 13C; U-99% 15N]	0.5 mM
9	DTT	no	1.0 mM
10	sodium phosphate	no	50 mM
11	sodium chloride	no	20 mM
12	sodium azide	no	0.05 %
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

10 2D 1H-15N HSQC_T1

Instrument

Varian INOVA - 600 MHz with cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.2, Details sodium phosphate buffer

#	Name	Isotope labeling	Concentration
8	SBDS	[U-99% 13C; U-99% 15N]	0.5 mM
9	DTT	no	1.0 mM
10	sodium phosphate	no	50 mM
11	sodium chloride	no	20 mM
12	sodium azide	no	0.05 %
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

11 2D 1H-15N HSQC_T1

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.2, Details sodium phosphate buffer

#	Name	Isotope labeling	Concentration
8	SBDS	[U-99% 13C; U-99% 15N]	0.5 mM
9	DTT	no	1.0 mM
10	sodium phosphate	no	50 mM
11	sodium chloride	no	20 mM
12	sodium azide	no	0.05 %
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

12 2D 1H-15N HSQC_T2

Instrument

Varian INOVA - 600 MHz with cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.2, Details sodium phosphate buffer

#	Name	Isotope labeling	Concentration
8	SBDS	[U-99% 13C; U-99% 15N]	0.5 mM
9	DTT	no	1.0 mM
10	sodium phosphate	no	50 mM
11	sodium chloride	no	20 mM
12	sodium azide	no	0.05 %
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

13 2D 1H-15N HSQC_T2

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.2, Details sodium phosphate buffer

#	Name	Isotope labeling	Concentration
8	SBDS	[U-99% 13C; U-99% 15N]	0.5 mM
9	DTT	no	1.0 mM
10	sodium phosphate	no	50 mM
11	sodium chloride	no	20 mM
12	sodium azide	no	0.05 %
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

14 2D 1H-15N HSQC_NOE

Instrument

Varian INOVA - 600 MHz with cryogenic probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.2, Details sodium phosphate buffer

#	Name	Isotope labeling	Concentration
8	SBDS	[U-99% 13C; U-99% 15N]	0.5 mM
9	DTT	no	1.0 mM
10	sodium phosphate	no	50 mM
11	sodium chloride	no	20 mM
12	sodium azide	no	0.05 %
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

15 2D 1H-15N HSQC_NOE

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.2, Details sodium phosphate buffer

#	Name	Isotope labeling	Concentration
8	SBDS	[U-99% 13C; U-99% 15N]	0.5 mM
9	DTT	no	1.0 mM
10	sodium phosphate	no	50 mM
11	sodium chloride	no	20 mM
12	sodium azide	no	0.05 %
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_16119_2kdo.nef
Input source #2: Coordindates	2kdo.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
GHMSIFTPTNQIRLTNVAVVRMKRAGKRFEIACYKNKVVGWRSGVEKDLDEVLQTHSVFVNVSKGQVAKKEDLISAFGTDDQTEICKQILTKGEVQVSDK
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GHMSIFTPTNQIRLTNVAVVRMKRAGKRFEIACYKNKVVGWRSGVEKDLDEVLQTHSVFVNVSKGQVAKKEDLISAFGTDDQTEICKQILTKGEVQVSDK

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

-------210-------220-------230-------240-------250--
SEDYGQQLEIVCLIDPGCFREIDELIKKETKGKGSLEVLNLKDVEEGDEKFE
||||||||||||||||||||||||||||||||||||||||||||||||||||
SEDYGQQLEIVCLIDPGCFREIDELIKKETKGKGSLEVLNLKDVEEGDEKFE

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	252	0	0	100.0

Content subtype: combined_16119_2kdo.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assignments_sbds	Warning	2292		91.3 (chain: A, length: 252)
1	Distance restraints	Discover_distance_constraints_2	Warning	3729 (1)	noe	91.7 (chain: A, length: 252)

Assigned chemical shifts

Saveframe: assignments_sbds
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 252, Sequence coverage: 91.3%
- Total number of assignments
  - ¹H chemical shifts: 1097
  - ¹³C chemical shifts: 979
  - ¹⁵N chemical shifts: 216
- 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)
7	THR	HG1	5.155
9	THR	HG1	5.17
15	THR	HG1	5.17

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1619	1056	65.2
¹³C chemical shifts	1182	979	82.8
¹⁵N chemical shifts	281	216	76.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	511	450	88.1
¹³C chemical shifts	504	458	90.9
¹⁵N chemical shifts	246	212	86.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1108	606	54.7
¹³C chemical shifts	678	521	76.8
¹⁵N chemical shifts	35	4	11.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	156	122	78.2
¹³C chemical shifts	156	124	79.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	72	20	27.8
¹³C chemical shifts	71	1	1.4
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: Discover_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 252, Sequence coverage: 91.7%
- Total number of restraints: 3729
- Weight of restraints: 1.0 (3729)
- Potential type of restraints: square-well-parabolic (3729)
- Range of distance target values: 1.98, 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

Keywords NMR protein structure, RNA-interacting protein, SBDS protein

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Found 1 Document (1.467 seconds)

BMRB: 16119

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles Swiss-Prot: 1 entries Detail

Related entities 1. SBDS, : 1 : 10 : 28 entities Detail

Interaction partners 1. SBDS, : 10 interactors Detail

Experiments performed 15 experiments Detail

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NMR combined restraints 3 contents Detail