BMRBj - BMREntryMaster

Found 1 Document (1.525 seconds)

BMRB: 15271

2JQ8

Solution structure of the Somatomedin B domain from vitronectin produced in Pichia pastoris

Authors

Kjaergaard, M., Gaardsvoll, H., Hirschberg, D., Nielbo, S., Mayasundari, A., Peterson, C.B., Jansson, A., Jorgensen, T.J.D., Poulsen, F.M., Ploug, M.

Assembly

SMB domain from vitronectin

Entity

1. SMB domain from vitronectin (polymer, Thiol state: all disulfide bound), 53 monomers, 6162.669 Da Detail

DQESCKGRCT EGFNVDKKCQ CDELCSYYQS CCTDYTAECK PQVTRGDHHH HHH

Formula weight

6162.669 Da

Entity Connection

disulfide 4 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS5:SG	1:CYS21:SG
2	disulfide	sing	1:CYS9:SG	1:CYS39:SG
3	disulfide	sing	1:CYS19:SG	1:CYS32:SG
4	disulfide	sing	1:CYS25:SG	1:CYS31:SG

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 84.9 %, Completeness: 75.5 %, Completeness (bb): 80.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	75.5 % (441 of 584)	76.1 % (232 of 305)	73.9 % (164 of 222)	78.9 % (45 of 57)
Backbone	80.1 % (253 of 316)	79.6 % (86 of 108)	78.8 % (123 of 156)	84.6 % (44 of 52)
Sidechain	72.0 % (229 of 318)	74.1 % (146 of 197)	70.7 % (82 of 116)	20.0 % (1 of 5)
Aromatic	48.3 % (28 of 58)	58.6 % (17 of 29)	37.9 % (11 of 29)
Methyl	90.9 % (20 of 22)	100.0 % (11 of 11)	81.8 % (9 of 11)

1. SMB

DQESCKGRCT EGFNVDKKCQ CDELCSYYQS CCTDYTAECK PQVTRGDHHH HHH

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details pH 6.5, no buffer, no salt

#	Name	Isotope labeling	Type	Concentration
1	SMB	[U-99% 13C; U-99% 15N]		0.4 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details ph 6.5, no buffer, no salt

#	Name	Isotope labeling	Concentration
2	SMB	natural abundance	0.7 mM
3	H2O	natural abundance	90 %
4	D2O		10 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.2514495
¹H	DSS	methyl protons	external	indirect	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: -0.04 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.2514495
¹H	DSS	methyl protons	external	indirect	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: -0.04 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.2514495
¹H	DSS	methyl protons	external	indirect	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: 0.07 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.2514495
¹H	DSS	methyl protons	external	indirect	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: -0.18 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2JQ8, Strand ID: A Detail

Release date

2007-12-18

Citation

Solution structure of recombinant somatomedin B domain from vitronectin produced in Pichia pastoris
Kjaergaard, M., Gaardsvoll, H., Hirschberg, D., Nielbo, S., Mayasundari, A., Peterson, C.B., Jansson, A., Jorgensen, T.J.D., Poulsen, F.M., Ploug, M.
Protein Sci. (2007), 16, 1934-1945, PubMed 17766387 , DOI 10.1110/ps.072949607 , Abstract

Related entities 1. SMB domain from vitronectin, : 1 : 5 : 18 entities Detail

Interaction partners 1. SMB domain from vitronectin, : 44 interactors Detail

More details for 44 interactors identified by 18 citations

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian Unity - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details pH 6.5, no buffer, no salt

#	Name	Isotope labeling	Type	Concentration
1	SMB	[U-99% 13C; U-99% 15N]		0.4 mM

2 3D HNCO

Instrument

Varian Unity - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details pH 6.5, no buffer, no salt

#	Name	Isotope labeling	Type	Concentration
1	SMB	[U-99% 13C; U-99% 15N]		0.4 mM

3 3D HNCA

Instrument

Varian Unity - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details pH 6.5, no buffer, no salt

#	Name	Isotope labeling	Type	Concentration
1	SMB	[U-99% 13C; U-99% 15N]		0.4 mM

4 3D HNCACB

Instrument

Varian Unity - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details pH 6.5, no buffer, no salt

#	Name	Isotope labeling	Type	Concentration
1	SMB	[U-99% 13C; U-99% 15N]		0.4 mM

5 3D HN(CO)CA

Instrument

Varian Unity - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details pH 6.5, no buffer, no salt

#	Name	Isotope labeling	Type	Concentration
1	SMB	[U-99% 13C; U-99% 15N]		0.4 mM

6 3D HN(COCA)CB

Instrument

Varian Unity - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details pH 6.5, no buffer, no salt

#	Name	Isotope labeling	Type	Concentration
1	SMB	[U-99% 13C; U-99% 15N]		0.4 mM

7 2D 1H-1H NOESY

Instrument

Varian Unity - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details ph 6.5, no buffer, no salt

#	Name	Isotope labeling	Concentration
2	SMB	natural abundance	0.7 mM
3	H2O	natural abundance	90 %
4	D2O		10 %

8 3D 1H-13C NOESY

Instrument

Varian Unity - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details pH 6.5, no buffer, no salt

#	Name	Isotope labeling	Type	Concentration
1	SMB	[U-99% 13C; U-99% 15N]		0.4 mM

9 3D 1H-15N NOESY

Instrument

Varian Unity - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details pH 6.5, no buffer, no salt

#	Name	Isotope labeling	Type	Concentration
1	SMB	[U-99% 13C; U-99% 15N]		0.4 mM

10 3D HCCH-TOCSY

Instrument

Varian Unity - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details pH 6.5, no buffer, no salt

#	Name	Isotope labeling	Type	Concentration
1	SMB	[U-99% 13C; U-99% 15N]		0.4 mM

11 3D 1H-15N TOCSY

Instrument

Varian Unity - 750 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details pH 6.5, no buffer, no salt

#	Name	Isotope labeling	Type	Concentration
1	SMB	[U-99% 13C; U-99% 15N]		0.4 mM

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_15271_2jq8.nef
Input source #2: Coordindates	2jq8.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:5:CYS:SG	A:21:CYS:SG	oxidized, CA 55.6, CB 40.31 ppm	oxidized, CA 54.65, CB 44.03 ppm	2.022
A:9:CYS:SG	A:39:CYS:SG	oxidized, CA 57.51, CB 37.8 ppm	oxidized, CA 52.53, CB 37.29 ppm	2.029
A:19:CYS:SG	A:32:CYS:SG	oxidized, CA 53.78, CB 42.98 ppm	oxidized, CA 55.18, CB 41.38 ppm	2.023
A:25:CYS:SG	A:31:CYS:SG	oxidized, CA 59.11, CB 39.63 ppm	oxidized, CA 54.47, CB 40.96 ppm	2.028

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---
DQESCKGRCTEGFNVDKKCQCDELCSYYQSCCTDYTAECKPQVTRGDHHHHHH
|||||||||||||||||||||||||||||||||||||||||||||||||||||
DQESCKGRCTEGFNVDKKCQCDELCSYYQSCCTDYTAECKPQVTRGDHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	53	0	0	100.0

Content subtype: combined_15271_2jq8.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	458		84.9 (chain: A, length: 53)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	994 (1)	noe	83.0 (chain: A, length: 53)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 53, Sequence coverage: 84.9%
- Total number of assignments
  - ¹H chemical shifts: 248
  - ¹³C chemical shifts: 166
  - ¹⁵N chemical shifts: 44
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	305	248	81.3
¹³C chemical shifts	222	166	74.8
¹⁵N chemical shifts	59	44	74.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	108	92	85.2
¹³C chemical shifts	106	84	79.2
¹⁵N chemical shifts	52	44	84.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	197	156	79.2
¹³C chemical shifts	116	82	70.7
¹⁵N chemical shifts	7	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	11	11	100.0
¹³C chemical shifts	11	9	81.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	29	16	55.2
¹³C chemical shifts	29	8	27.6

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 53, Sequence coverage: 83.0%
- Total number of restraints: 994
- Weight of restraints: 1.0 (994)
- Potential type of restraints: upper-bound-parabolic (994)
- Range of distance target values: 2.35, 6.5 (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

Keywords disulfide-rich domain, NMR, PAI-1, SMB, somatomedin B, uPAR, vitronectin, somatomedin B domain

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Found 1 Document (1.525 seconds)

BMRB: 15271

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. SMB domain from vitronectin, : 1 : 5 : 18 entities Detail

Interaction partners 1. SMB domain from vitronectin, : 44 interactors Detail

Experiments performed 11 experiments Detail

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NMR combined restraints 3 contents Detail