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BMRB: 17391

2L83

A protein from Haloferax volcanii

Authors

Zhang, W., Liao, S., Fan, K., Tu, X.

Assembly

protein from Haloferax volcanii

Entity

1. protein from Haloferax volcanii (polymer), 174 monomers, 17855.43 Da Detail

MEWKLFADLA EVAGSRTVRV DVDGDATVGD ALDALVGAHP ALESRVFGDD GELYDHINVL RNGEAAALGE ATAAGDELAL FPPVSGGMEW KLFADLAEVA GSRTVRVDVD GDATVGDALD ALVGAHPALE SRVFGDDGEL YDHINVLRNG EAAALGEATA AGDELALFPP VSGG

Formula weight

17855.43 Da

Source organism

Haloferax volcanii

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 55.7 %, Completeness: 39.6 %, Completeness (bb): 48.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	39.6 % (708 of 1788)	41.9 % (376 of 898)	33.9 % (243 of 716)	51.1 % (89 of 174)
Backbone	48.4 % (499 of 1032)	50.8 % (185 of 364)	45.0 % (225 of 500)	53.0 % (89 of 168)
Sidechain	31.6 % (287 of 908)	36.0 % (192 of 534)	25.8 % (95 of 368)	0.0 % (0 of 6)
Aromatic	0.0 % (0 of 116)	0.0 % (0 of 58)	0.0 % (0 of 56)	0.0 % (0 of 2)
Methyl	41.4 % (96 of 232)	56.0 % (65 of 116)	26.7 % (31 of 116)

1. entity

MEWKLFADLA EVAGSRTVRV DVDGDATVGD ALDALVGAHP ALESRVFGDD GELYDHINVL RNGEAAALGE ATAAGDELAL FPPVSGGMEW KLFADLAEVA GSRTVRVDVD GDATVGDALD ALVGAHPALE SRVFGDDGEL YDHINVLRNG EAAALGEATA AGDELALFPP VSGG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	100 mM
2	sodium phosphate	natural abundance	20 mM
3	protein from Haloferax volcanii		0.6 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
6	sodium chloride	natural abundance	100 mM
7	sodium phosphate	natural abundance	20 mM
8	protein from Haloferax volcanii		0.6 mM
9	D2O	natural abundance	100 %

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
³¹P	DSS	methyl protons	null	indirect	0.4048086

Referencing offset: -0.34 ppm, Outliers: 1 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
³¹P	DSS	methyl protons	null	indirect	0.4048086

Referencing offset: -0.34 ppm, Outliers: 1 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
³¹P	DSS	methyl protons	null	indirect	0.4048086

Referencing offset: 0.04 ppm, Outliers: 1 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
³¹P	DSS	methyl protons	null	indirect	0.4048086

Referencing offset: -0.09 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2L83, Strand ID: A Detail

Release date

2012-01-10

Citation

Ionic strength-dependent conformations of a ubiquitin-like small archaeal modifier protein (SAMP1) from Haloferax volcanii
Ye, K., Liao, S., Zhang, W., Fan, K., Zhang, X., Zhang, J., Xu, C., Tu, X.
Protein Sci. (2013), 22, 1174-1182, PubMed 23818097 , DOI 10.1002/pro.2302 , Abstract

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DMX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	100 mM
2	sodium phosphate	natural abundance	20 mM
3	protein from Haloferax volcanii		0.6 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

2 3D CBCA(CO)NH

Instrument

Bruker DMX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	100 mM
2	sodium phosphate	natural abundance	20 mM
3	protein from Haloferax volcanii		0.6 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

3 3D C(CO)NH

Instrument

Bruker DMX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	100 mM
2	sodium phosphate	natural abundance	20 mM
3	protein from Haloferax volcanii		0.6 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

4 3D HNCO

Instrument

Bruker DMX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	100 mM
2	sodium phosphate	natural abundance	20 mM
3	protein from Haloferax volcanii		0.6 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

5 3D HNCACB

Instrument

Bruker DMX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	100 mM
2	sodium phosphate	natural abundance	20 mM
3	protein from Haloferax volcanii		0.6 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

6 3D HBHA(CO)NH

Instrument

Bruker DMX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	100 mM
2	sodium phosphate	natural abundance	20 mM
3	protein from Haloferax volcanii		0.6 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

7 3D HN(CO)CA

Instrument

Bruker DMX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	100 mM
2	sodium phosphate	natural abundance	20 mM
3	protein from Haloferax volcanii		0.6 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

8 3D H(CCO)NH

Instrument

Bruker DMX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	100 mM
2	sodium phosphate	natural abundance	20 mM
3	protein from Haloferax volcanii		0.6 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

9 3D HCCH-TOCSY

Instrument

Bruker DMX - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
6	sodium chloride	natural abundance	100 mM
7	sodium phosphate	natural abundance	20 mM
8	protein from Haloferax volcanii		0.6 mM
9	D2O	natural abundance	100 %

10 3D HCCH-COSY

Instrument

Bruker DMX - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
6	sodium chloride	natural abundance	100 mM
7	sodium phosphate	natural abundance	20 mM
8	protein from Haloferax volcanii		0.6 mM
9	D2O	natural abundance	100 %

11 3D 1H-13C NOESY

Instrument

Bruker DMX - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
6	sodium chloride	natural abundance	100 mM
7	sodium phosphate	natural abundance	20 mM
8	protein from Haloferax volcanii		0.6 mM
9	D2O	natural abundance	100 %

12 3D 1H-15N NOESY

Instrument

Bruker DMX - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	sodium chloride	natural abundance	100 mM
2	sodium phosphate	natural abundance	20 mM
3	protein from Haloferax volcanii		0.6 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17391_2l83.nef
Input source #2: Coordindates	2l83.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-----
MEWKLFADLAEVAGSRTVRVDVDGDATVGDALDALVGAHPALESRVFGDDGELYDHINVLRNGEAAALGEATAAGDELALFPPVSGGLEHHHHHH
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MEWKLFADLAEVAGSRTVRVDVDGDATVGDALDALVGAHPALESRVFGDDGELYDHINVLRNGEAAALGEATAAGDELALFPPVSGGLEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	95	0	0	100.0

Content subtype: combined_17391_2l83.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	565		84.2 (chain: A, length: 95)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	930 (1)	noe	86.3 (chain: A, length: 95)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	26 (1)	hbond	17.9 (chain: A, length: 95)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	95 (95)	.	77.9 (chain: A, length: 95)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 95, Sequence coverage: 84.2%
- Total number of assignments
  - ¹H chemical shifts: 307
  - ¹³C chemical shifts: 183
  - ¹⁵N chemical shifts: 75
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- 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)
27	THR	HG1	7.021

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	498	306	61.4
¹³C chemical shifts	398	183	46.0
¹⁵N chemical shifts	99	75	75.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	198	152	76.8
¹³C chemical shifts	190	118	62.1
¹⁵N chemical shifts	92	75	81.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	300	154	51.3
¹³C chemical shifts	208	65	31.2
¹⁵N chemical shifts	7	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	61	51	83.6
¹³C chemical shifts	61	14	23.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	41	0	0.0
¹³C chemical shifts	40	0	0.0
¹⁵N chemical shifts	1	0	0.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 95, Sequence coverage: 86.3%
- Total number of restraints: 930
- Weight of restraints: 1.0 (930)
- Potential type of restraints: square-well-parabolic (930)
- Range of distance target values: 2.4, 4.15 (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
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 95, Sequence coverage: 17.9%
  - Total number of restraints: 26
  - Weight of restraints: 1.0 (26)
  - Potential type of restraints: square-well-parabolic (26)
  - Range of distance target values: 2.3, 3.4 (Å)
  - Histogram of 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: 95, Sequence coverage: 77.9%
- Total number of restraints: 95
- Total number of restraints per polymer type: 95
- Weight of restraints: 1.0 (95)
- Potential type of restraints: square-well-parabolic (95)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords NMR, protein binding

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Found 1 Document (0.721 seconds)

BMRB: 17391

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Experiments performed 12 experiments Detail

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NMR combined restraints 5 contents Detail