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Found 1 Document (0.654 seconds)

BMRB: 18856

2M1C

HADDOCK structure of GtYybT PAS Homodimer

Authors

Liang, Z.X., Pervushin, K., Tan, E., Rao, F., Pasunooti, S., Soehano, I., Lescar, J.

Assembly

GtYybT PAS Homodimer

Entity

1. GtYybT PAS Homodimer (polymer), 113 monomers, 13188.16 × 2 Da Detail

RGSHMRSLHK ELQQYISNLS YRVKKVSEEA LMQMPIGILL LDEEDKIEWS NRFLAACFKE QTLIGRSLAE LSEPLAAFVK KGKTDEEIIE LNGKQLKVIV HRHERLLYFF DVT

Total weight

26376.32 Da

Max. entity weight

13188.16 Da

Source organism

Geobacillus thermodenitrificans

Exptl. method

solution NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.1 %, Completeness: 94.1 %, Completeness (bb): 97.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	94.1 % (1312 of 1395)	95.5 % (699 of 732)	91.3 % (496 of 543)	97.5 % (117 of 120)
Backbone	97.3 % (656 of 674)	96.5 % (221 of 229)	97.9 % (327 of 334)	97.3 % (108 of 111)
Sidechain	91.9 % (762 of 829)	95.0 % (478 of 503)	86.8 % (275 of 317)	100.0 % (9 of 9)
Aromatic	80.4 % (82 of 102)	92.2 % (47 of 51)	68.0 % (34 of 50)	100.0 % (1 of 1)
Methyl	98.6 % (136 of 138)	97.1 % (67 of 69)	100.0 % (69 of 69)

1. PAS domain of DHH subfamily 1 protein

RGSHMRSLHK ELQQYISNLS YRVKKVSEEA LMQMPIGILL LDEEDKIEWS NRFLAACFKE QTLIGRSLAE LSEPLAAFVK KGKTDEEIIE LNGKQLKVIV HRHERLLYFF DVT

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2, Details 50mM phosphate buffer NA; 95% H2O, 5% D2O, pH 6.5, 200mM NaCl, 1x protease inhibitor

#	Name	Isotope labeling	Concentration
1	PAS domain of DHH subfamily 1 protein	[U-99% 13C; U-99% 15N]	0.7 mM
2	phosphate buffer	natural abundance	50 mM
3	NaCl	natural abundance	200 mM

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: 0.33 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

Referencing offset: 0.33 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

Referencing offset: 0.09 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: 1.5 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 4 models in PDB: 2M1C, Strand ID: A, B Detail

Release date

2013-03-24

Citation

Solution structure of the PAS domain of a thermophilic YybT protein homolog reveals a potential ligand-binding site
Tan, E., Rao, F., Pasunooti, S., Pham, T., Soehano, I., Turner, M.S., Liew, C., Lescar, J., Pervushin, K., Liang, Z.
J. Biol. Chem. (2013), 288, 11949-11959, PubMed 23504327 , DOI 10.1074/jbc.M112.437764 , Abstract

Related entities 1. GtYybT PAS Homodimer, : 1 : 6 entities Detail

Experiments performed 10 experiments Detail

1 2D_15N_TROSY-HSQC

Instrument

Bruker AVANCE II - na MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2, Details 50mM phosphate buffer NA; 95% H2O, 5% D2O, pH 6.5, 200mM NaCl, 1x protease inhibitor

#	Name	Isotope labeling	Concentration
1	PAS domain of DHH subfamily 1 protein	[U-99% 13C; U-99% 15N]	0.7 mM
2	phosphate buffer	natural abundance	50 mM
3	NaCl	natural abundance	200 mM

2 2D_13C_HMQC

Instrument

Bruker AVANCE II - na MHz

Sample

#	Name	Isotope labeling	Concentration
1	PAS domain of DHH subfamily 1 protein	[U-99% 13C; U-99% 15N]	0.7 mM
2	phosphate buffer	natural abundance	50 mM
3	NaCl	natural abundance	200 mM

3 3D_HNCA

Instrument

Bruker AVANCE II - na MHz

Sample

#	Name	Isotope labeling	Concentration
1	PAS domain of DHH subfamily 1 protein	[U-99% 13C; U-99% 15N]	0.7 mM
2	phosphate buffer	natural abundance	50 mM
3	NaCl	natural abundance	200 mM

4 3D_HN(CO)CA

Instrument

Bruker AVANCE II - na MHz

Sample

#	Name	Isotope labeling	Concentration
1	PAS domain of DHH subfamily 1 protein	[U-99% 13C; U-99% 15N]	0.7 mM
2	phosphate buffer	natural abundance	50 mM
3	NaCl	natural abundance	200 mM

5 3D_HNCO

Instrument

Bruker AVANCE II - na MHz

Sample

#	Name	Isotope labeling	Concentration
1	PAS domain of DHH subfamily 1 protein	[U-99% 13C; U-99% 15N]	0.7 mM
2	phosphate buffer	natural abundance	50 mM
3	NaCl	natural abundance	200 mM

6 3D_HN(CA)CO

Instrument

Bruker AVANCE II - na MHz

Sample

#	Name	Isotope labeling	Concentration
1	PAS domain of DHH subfamily 1 protein	[U-99% 13C; U-99% 15N]	0.7 mM
2	phosphate buffer	natural abundance	50 mM
3	NaCl	natural abundance	200 mM

7 3D_CBCA(CO)NH

Instrument

Bruker AVANCE II - na MHz

Sample

#	Name	Isotope labeling	Concentration
1	PAS domain of DHH subfamily 1 protein	[U-99% 13C; U-99% 15N]	0.7 mM
2	phosphate buffer	natural abundance	50 mM
3	NaCl	natural abundance	200 mM

8 3D_HN(CA)CB

Instrument

Bruker AVANCE II - na MHz

Sample

#	Name	Isotope labeling	Concentration
1	PAS domain of DHH subfamily 1 protein	[U-99% 13C; U-99% 15N]	0.7 mM
2	phosphate buffer	natural abundance	50 mM
3	NaCl	natural abundance	200 mM

9 3D_15N-separated_NOESY

Instrument

Bruker AVANCE II - na MHz

Sample

#	Name	Isotope labeling	Concentration
1	PAS domain of DHH subfamily 1 protein	[U-99% 13C; U-99% 15N]	0.7 mM
2	phosphate buffer	natural abundance	50 mM
3	NaCl	natural abundance	200 mM

10 3D_13C-separated_NOESY

Instrument

Bruker AVANCE II - na MHz

Sample

#	Name	Isotope labeling	Concentration
1	PAS domain of DHH subfamily 1 protein	[U-99% 13C; U-99% 15N]	0.7 mM
2	phosphate buffer	natural abundance	50 mM
3	NaCl	natural abundance	200 mM

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_18856_2m1c.nef
Input source #2: Coordindates	2m1c.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

-50-------60--------70--------80--------90-------100-------110-------120-------130-------140-------1
RGSHMRSLHKELQQYISNLSYRVKKVSEEALMQMPIGILLLDEEDKIEWSNRFLAACFKEQTLIGRSLAELSEPLAAFVKKGKTDEEIIELNGKQLKVIV
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
RGSHMRSLHKELQQYISNLSYRVKKVSEEALMQMPIGILLLDEEDKIEWSNRFLAACFKEQTLIGRSLAELSEPLAAFVKKGKTDEEIIELNGKQLKVIV
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

50-------160-
HRHERLLYFFDVT
|||||||||||||
HRHERLLYFFDVT
-------110---

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

-50-------60--------70--------80--------90-------100-------110-------120-------130-------140-------1
RGSHMRSLHKELQQYISNLSYRVKKVSEEALMQMPIGILLLDEEDKIEWSNRFLAACFKEQTLIGRSLAELSEPLAAFVKKGKTDEEIIELNGKQLKVIV
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
RGSHMRSLHKELQQYISNLSYRVKKVSEEALMQMPIGILLLDEEDKIEWSNRFLAACFKEQTLIGRSLAELSEPLAAFVKKGKTDEEIIELNGKQLKVIV
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

50-------160-
HRHERLLYFFDVT
|||||||||||||
HRHERLLYFFDVT
-------110---

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	113	0	0	100.0
B	B	113	0	0	100.0

Content subtype: combined_18856_2m1c.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1341		99.1 (chain: A, length: 113)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	220 (1)	noe	51.3 (chain: B, length: 113)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 113, Sequence coverage: 99.1%
- Total number of assignments
  - ¹H chemical shifts: 721
  - ¹³C chemical shifts: 498
  - ¹⁵N chemical shifts: 122
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
114	ARG	HH11	6.56
114	ARG	HH12	6.56
114	ARG	HH21	6.734
114	ARG	HH22	6.734
115	SER	HG	7.221
120	SER	HG	6.328
150	ARG	HH11	6.449
150	ARG	HH12	6.449
150	ARG	HH21	6.698
150	ARG	HH22	6.698

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	732	711	97.1
¹³C chemical shifts	543	498	91.7
¹⁵N chemical shifts	127	122	96.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	229	225	98.3
¹³C chemical shifts	226	222	98.2
¹⁵N chemical shifts	111	108	97.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	503	486	96.6
¹³C chemical shifts	317	276	87.1
¹⁵N chemical shifts	16	14	87.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	72	72	100.0
¹³C chemical shifts	72	72	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	51	47	92.2
¹³C chemical shifts	50	33	66.0
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 113, Sequence coverage: 51.3%
- Total number of restraints: 220
- Weight of restraints: 1.0 (220)
- Potential type of restraints: upper-bound-parabolic (220)
- Range of distance target values: 1.0, 5.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
    None
  - Chain_ID: B
- Distance restraints on contact map

Keywords ligand binding, PAS domain, YybT

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Found 1 Document (0.654 seconds)

BMRB: 18856

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. GtYybT PAS Homodimer, : 1 : 6 entities Detail

Experiments performed 10 experiments Detail

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NMR combined restraints 3 contents Detail