BMRBj - BMREntryMaster

Found 1 Document (0.602 seconds)

BMRB: 16153

2KEL

Structure of the transcription repressor SvtR08 (gp08) from the hyperthermophilic archaeal virus SIRV1

Authors

Guilliere, F., Kessler, A., Peixeiro, N., Sezonov, G., Prangishvili, D., Delepierre, M., Guijarro, J.I.

Assembly

SvtR08

Entity

1. SvtR08 (polymer, Thiol state: all free), 56 monomers, 6620.628 × 2 Da Detail

MQTQEQSQKK KQKAVFGIYM DKDLKTRLKV YCAKNNLQLT QAIEEAIKEY LQKRNG

Total weight

13241.256 Da

Max. entity weight

6620.628 Da

Source organism

Sulfolobus islandicus rod-shaped virus 1

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.2 %, Completeness: 96.2 %, Completeness (bb): 97.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	96.2 % (687 of 714)	96.3 % (369 of 383)	97.0 % (256 of 264)	92.5 % (62 of 67)
Backbone	97.3 % (327 of 336)	97.4 % (111 of 114)	97.6 % (162 of 166)	96.4 % (54 of 56)
Sidechain	95.6 % (413 of 432)	95.9 % (258 of 269)	96.7 % (147 of 152)	72.7 % (8 of 11)
Aromatic	97.1 % (33 of 34)	100.0 % (17 of 17)	94.1 % (16 of 17)
Methyl	100.0 % (54 of 54)	100.0 % (27 of 27)	100.0 % (27 of 27)

1. svtr08

MQTQEQSQKK KQKAVFGIYM DKDLKTRLKV YCAKNNLQLT QAIEEAIKEY LQKRNG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 5.5

#	Name	Isotope labeling	Concentration
1	svtr08	natural abundance	1.6 mM
2	sodium acetate	[U-2H]	20 mM
3	D2O	natural abundance	10 %
4	H2O	natural abundance	90 %

Sample #2

Solvent system 100% D2O, Pressure 1.0 atm, Temperature 298 K, pH 5.5

#	Name	Isotope labeling	Concentration
5	svtr08	natural abundance	1.2 mM
6	sodium acetate	[U-2H]	20 mM
7	D2O	natural abundance	100 %

Sample #3

Solvent system 88% H2O/12% D2O, Pressure 1.0 atm, Temperature 298 K, pH 5.5

#	Name	Isotope labeling	Concentration
8	svtr08	[U-98% 13C; U-98% 15N]	1.5 mM
9	sodium acetate	[U-2H]	20 mM
10	D2O	natural abundance	12 %
11	H2O	natural abundance	88 %

Sample #4

Solvent system 88% H2O/12% D2O, Pressure 1.0 atm, Temperature 298 K, pH 5.5

#	Name	Isotope labeling	Concentration
12	svtr08	50%[U-98% 13C; U-98% 15N]; 50% natural abundance	2.9 mM
13	sodium acetate	[U-2H]	20 mM
14	D2O	natural abundance	12 %
15	H2O	natural abundance	88 %

Sample #5

Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 5.5

#	Name	Isotope labeling	Concentration
16	svtr08	[U-98% 15N]	1.7 mM
17	sodium acetate	[U-2H]	20 mM
18	D2O	natural abundance	10 %
19	H2O	natural abundance	90 %

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: -0.09 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: -0.09 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: 0.07 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

Referencing offset: 0.07 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2KEL, Strand ID: A, B Detail

Release date

2009-06-25

Citation

Structure, function, and targets of the transcriptional regulator SvtR from the hyperthermophilic archaeal virus SIRV1
Guilliere, F., Peixeiro, N., Kessler, A., Raynal, B., Desnoues, N., Keller, J., Delepierre, M., Prangishvili, D., Sezonov, G., Guijarro, J.
J. Biol. Chem. (2009), 284, 22222-22237, PubMed 19535331 , DOI 10.1074/jbc.M109.029850 , Abstract

Related entities 1. SvtR08, : 1 : 1 : 8 entities Detail

Experiments performed 5 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16153_2kel.nef
Input source #2: Coordindates	2kel.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------
MQTQEQSQKKKQKAVFGIYMDKDLKTRLKVYCAKNNLQLTQAIEEAIKEYLQKRNG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MQTQEQSQKKKQKAVFGIYMDKDLKTRLKVYCAKNNLQLTQAIEEAIKEYLQKRNG

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

--------10--------20--------30--------40--------50------
MQTQEQSQKKKQKAVFGIYMDKDLKTRLKVYCAKNNLQLTQAIEEAIKEYLQKRNG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MQTQEQSQKKKQKAVFGIYMDKDLKTRLKVYCAKNNLQLTQAIEEAIKEYLQKRNG

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	56	0	0	100.0
B	B	56	0	0	100.0

Content subtype: combined_16153_2kel.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	694		98.2 (chain: A, length: 56)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	8574 (1)	noe	82.1 (chain: A, length: 56), 82.1 (chain: B, length: 56)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	54 (1)	hbond	66.1 (chain: A, length: 56), 66.1 (chain: B, length: 56)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	56 (56)	.	64.3 (chain: A, length: 56), 64.3 (chain: B, length: 56)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 56, Sequence coverage: 98.2%
- Total number of assignments
  - ¹H chemical shifts: 369
  - ¹³C chemical shifts: 261
  - ¹⁵N chemical shifts: 64
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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)
35	ASN	CG	176.95
36	ASN	CG	178.452
38	GLN	CD	180.315
52	GLN	CD	178.535
55	ASN	CG	178.484

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	383	369	96.3
¹³C chemical shifts	264	256	97.0
¹⁵N chemical shifts	69	64	92.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	114	111	97.4
¹³C chemical shifts	112	109	97.3
¹⁵N chemical shifts	56	54	96.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	269	258	95.9
¹³C chemical shifts	152	147	96.7
¹⁵N chemical shifts	13	10	76.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	29	28	96.6
¹³C chemical shifts	29	28	96.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	17	17	100.0
¹³C chemical shifts	17	16	94.1

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 56, Sequence coverage: 82.1%
  - Entity_assembly_ID: B, Chain length: 56, Sequence coverage: 82.1%
- Total number of restraints: 8363
- Weight of restraints: 1.0 (8363)
- Potential type of restraints: square-well-parabolic (8363)
- Range of distance target values: 1.22, 9.26 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 56, Sequence coverage: 66.1%
    - Entity_assembly_ID: B, Chain length: 56, Sequence coverage: 66.1%
  - Total number of restraints: 54
  - Weight of restraints: 1.0 (54)
  - Potential type of restraints: square-well-parabolic (54)
  - Range of distance target values: 2.0, 2.0 (Å)
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - 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: 56, Sequence coverage: 64.3%
  - Entity_assembly_ID: B, Chain length: 56, Sequence coverage: 64.3%
- Total number of restraints: 56
- Total number of restraints per polymer type: 56
- Weight of restraints: 1.0 (56)
- Potential type of restraints: square-well-parabolic (56)
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

Keywords HOMODIMER, PROTEIN, RIBBON-HELIX-HELIX

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.602 seconds)

BMRB: 16153

Sample #1

Sample #2

Sample #3

Sample #4

Sample #5

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. SvtR08, : 1 : 1 : 8 entities Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail