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BMRB: 25147

2MT3

Struture of -24 DNA binding domain of sigma 54 from E. coli

Authors

Wemmer, D., Gao, Z., Pelton, J.

Assembly

DNA binding domain of sigma 54 from E.coli

Entity

1. DNA binding domain of sigma 54 from E.coli (polymer, Thiol state: not present), 84 monomers, 9142.336 Da Detail

EASSTAIRAL VKKLIAAENP AKPLSDSKLT SLLSEQGIMV ARRTVAKYRE SLSIPPSNQR KQLVANSSSV DKLAAALEHH HHHH

Formula weight

9142.336 Da

Source organism

Escherichia coli

Exptl. method

Refine. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 91.7 %, Completeness: 80.6 %, Completeness (bb): 81.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	80.6 % (768 of 953)	81.7 % (405 of 496)	78.2 % (290 of 371)	84.9 % (73 of 86)
Backbone	81.7 % (405 of 496)	87.3 % (144 of 165)	74.9 % (188 of 251)	91.3 % (73 of 80)
Sidechain	80.4 % (434 of 540)	78.9 % (261 of 331)	85.2 % (173 of 203)	0.0 % (0 of 6)
Aromatic	25.0 % (8 of 32)	25.0 % (4 of 16)	25.0 % (4 of 16)
Methyl	94.3 % (100 of 106)	94.3 % (50 of 53)	94.3 % (50 of 53)

1. entity

EASSTAIRAL VKKLIAAENP AKPLSDSKLT SLLSEQGIMV ARRTVAKYRE SLSIPPSNQR KQLVANSSSV DKLAAALEHH HHHH

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity			0.0 ~ 0.0 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		200 mM
4	DTT	natural abundance		1 mM

LACS Plot; CA

Referencing offset: -0.19 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: -0.19 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: 0.08 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: -0.04 ppm, Outliers: 5 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2MT3, Strand ID: A Detail

Release date

2015-08-23

Citation

Struture of -24 DNA binding domain of sigma 54 from E. coli
Gao, Z., Pelton, J., Wemmer, D.
Not known

Experiments performed 14 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity			0.0 ~ 0.0 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		200 mM
4	DTT	natural abundance		1 mM

2 3D CBCA(CO)NH

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity			0.0 ~ 0.0 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		200 mM
4	DTT	natural abundance		1 mM

3 3D C(CO)NH

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity			0.0 ~ 0.0 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		200 mM
4	DTT	natural abundance		1 mM

4 3D HNCA

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity			0.0 ~ 0.0 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		200 mM
4	DTT	natural abundance		1 mM

5 3D HNCACB

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity			0.0 ~ 0.0 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		200 mM
4	DTT	natural abundance		1 mM

6 3D H(CCO)NH

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity			0.0 ~ 0.0 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		200 mM
4	DTT	natural abundance		1 mM

7 3D HCCH-TOCSY

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity			0.0 ~ 0.0 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		200 mM
4	DTT	natural abundance		1 mM

8 3D HNHA

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity			0.0 ~ 0.0 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		200 mM
4	DTT	natural abundance		1 mM

9 3D 1H-15N NOESY

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity			0.0 ~ 0.0 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		200 mM
4	DTT	natural abundance		1 mM

10 3D 1H-15N TOCSY

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity			0.0 ~ 0.0 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		200 mM
4	DTT	natural abundance		1 mM

11 3D 1H-13C NOESY aliphatic

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity			0.0 ~ 0.0 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		200 mM
4	DTT	natural abundance		1 mM

12 3D HCCH-COSY

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity			0.0 ~ 0.0 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		200 mM
4	DTT	natural abundance		1 mM

13 3D HCACO

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity			0.0 ~ 0.0 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		200 mM
4	DTT	natural abundance		1 mM

14 3D HNCO

Instrument

Bruker DRX - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	entity			0.0 ~ 0.0 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		200 mM
4	DTT	natural abundance		1 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25147_2mt3.nef
Input source #2: Coordindates	2mt3.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

----420-------430-------440-------450-------460-------470-------480-------490-------
EASSTAIRALVKKLIAAENPAKPLSDSKLTSLLSEQGIMVARRTVAKYRESLSIPPSNQRKQLVANSSSVDKLAAALEHHHHHH
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
EASSTAIRALVKKLIAAENPAKPLSDSKLTSLLSEQGIMVARRTVAKYRESLSIPPSNQRKQLVANSSSVDKLAAALEHHHHHH
--------10--------20--------30--------40--------50--------60--------70--------80----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	84	0	0	100.0

Content subtype: combined_25147_2mt3.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	764		89.3 (chain: A, length: 84)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	737 (1)	noe	90.5 (chain: A, length: 84)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	119 (119)	.	88.1 (chain: A, length: 84)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 84, Sequence coverage: 89.3%
- Total number of assignments
  - ¹H chemical shifts: 412
  - ¹³C chemical shifts: 281
  - ¹⁵N chemical shifts: 71
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 84, Sequence coverage: 90.5%
- Total number of restraints: 736
- Weight of restraints: 1.0 (736)
- Potential type of restraints: upper-bound-parabolic (736)
- Range of distance target values: 2.5, 5.0 (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

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 84, Sequence coverage: 88.1%
- Total number of restraints: 119
- Total number of restraints per polymer type: 119
- Weight of restraints: 1.0 (119)
- Potential type of restraints: square-well-parabolic (119)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Protein