BMRBj - BMREntryMaster

Found 1 Document (0.709 seconds)

BMRB: 15926

2K7R

N-terminal domain of the Bacillus subtilis helicase-loading protein DnaI

Authors

Loscha, K.V., Jaudzems, K., Ioannou, C., Su, X., Dixon, N.E.

Assembly

DnaI N-domain

Entity

1. DnaI N-domain (polymer, Thiol state: free and other bound), 106 monomers, 12525.11 Da Detail

MEPIGRSLQG VTGRPDFQKR LEQMKEKVMK DQDVQAFLKE NEEVIDQKMI EKSLNKLYEY IEQSKNCSYC SEDENCNNLL EGYHPKLVVN GRSIDIEYYE CPVKRK

2. ZN (non-polymer), 65.409 Da

Total weight

12590.52 Da

Max. entity weight

12525.11 Da

Entity Connection

ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:CYS67:SG	2:ZN1:ZN
2	na	sing	1:CYS70:SG	2:ZN1:ZN
3	na	sing	1:HIS84:NE2	2:ZN1:ZN
4	na	sing	1:CYS101:SG	2:ZN1:ZN

Source organism

Bacillus subtilis

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 97.2 %, Completeness (bb): 98.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹⁵N
All	97.2 % (787 of 810)	97.0 % (673 of 694)	98.3 % (114 of 116)
Backbone	98.1 % (309 of 315)	98.1 % (209 of 213)	98.0 % (100 of 102)
Sidechain	96.6 % (478 of 495)	96.5 % (464 of 481)	100.0 % (14 of 14)
Aromatic	100.0 % (36 of 36)	100.0 % (36 of 36)
Methyl	97.7 % (43 of 44)	97.7 % (43 of 44)

1. DnaI N-domain

MEPIGRSLQG VTGRPDFQKR LEQMKEKVMK DQDVQAFLKE NEEVIDQKMI EKSLNKLYEY IEQSKNCSYC SEDENCNNLL EGYHPKLVVN GRSIDIEYYE CPVKRK

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 (±0.1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-95% 15N]		0.5 (±0.05) mM
2	ZINC ION	natural abundance		0.5 (±0.05) mM
3	D2O	[U-99% 2H]		10 (±0.5) %
4	H2O	natural abundance		90 (±0.5) %
5	sodium phosphate	natural abundance		10 (±0.2) mM
6	sodium azide	natural abundance		0.1 (±0.01) %
7	sodium chloride	natural abundance		100 (±1.0) mM
8	DTT	natural abundance		1 (±0.05) mM

Protein Blocks Logo

Calculated from 20 models in PDB: 2K7R, Strand ID: A Detail

Release date

2009-04-03

Citation

A novel zinc-binding fold in the helicase interaction domain of the Bacillus subtilis DnaI helicase loader
Loscha, K.V., Jaudzems, K., Ioannou, C., Su, X., Hill, F.R., Otting, G., Dixon, N.E., Liepinsh, E.
Nucleic Acids Res. (2009), 37, 2395-2404, PubMed 19255093 , DOI 10.1093/nar/gkp092 , Abstract

Related entities 1. DnaI N-domain, : 1 : 2 : 3 entities Detail

Interaction partners 1. DnaI N-domain, : 4 interactors Detail

More details for 4 interactors identified by 1 citations

Experiments performed 7 experiments Detail

1 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz TCI cryoprobes

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 (±0.1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-95% 15N]		0.5 (±0.05) mM
2	ZINC ION	natural abundance		0.5 (±0.05) mM
3	D2O	[U-99% 2H]		10 (±0.5) %
4	H2O	natural abundance		90 (±0.5) %
5	sodium phosphate	natural abundance		10 (±0.2) mM
6	sodium azide	natural abundance		0.1 (±0.01) %
7	sodium chloride	natural abundance		100 (±1.0) mM
8	DTT	natural abundance		1 (±0.05) mM

2 3D HNHA

Instrument

Bruker Avance - 800 MHz TCI cryoprobes

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 (±0.1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-95% 15N]		0.5 (±0.05) mM
2	ZINC ION	natural abundance		0.5 (±0.05) mM
3	D2O	[U-99% 2H]		10 (±0.5) %
4	H2O	natural abundance		90 (±0.5) %
5	sodium phosphate	natural abundance		10 (±0.2) mM
6	sodium azide	natural abundance		0.1 (±0.01) %
7	sodium chloride	natural abundance		100 (±1.0) mM
8	DTT	natural abundance		1 (±0.05) mM

3 2D 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz TCI cryoprobes

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 (±0.1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-95% 15N]		0.5 (±0.05) mM
2	ZINC ION	natural abundance		0.5 (±0.05) mM
3	D2O	[U-99% 2H]		10 (±0.5) %
4	H2O	natural abundance		90 (±0.5) %
5	sodium phosphate	natural abundance		10 (±0.2) mM
6	sodium azide	natural abundance		0.1 (±0.01) %
7	sodium chloride	natural abundance		100 (±1.0) mM
8	DTT	natural abundance		1 (±0.05) mM

4 2D DQF-COSY

Instrument

Bruker Avance - 800 MHz TCI cryoprobes

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 (±0.1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-95% 15N]		0.5 (±0.05) mM
2	ZINC ION	natural abundance		0.5 (±0.05) mM
3	D2O	[U-99% 2H]		10 (±0.5) %
4	H2O	natural abundance		90 (±0.5) %
5	sodium phosphate	natural abundance		10 (±0.2) mM
6	sodium azide	natural abundance		0.1 (±0.01) %
7	sodium chloride	natural abundance		100 (±1.0) mM
8	DTT	natural abundance		1 (±0.05) mM

5 2D 1H-1H TOCSY

Instrument

Bruker Avance - 800 MHz TCI cryoprobes

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 (±0.1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-95% 15N]		0.5 (±0.05) mM
2	ZINC ION	natural abundance		0.5 (±0.05) mM
3	D2O	[U-99% 2H]		10 (±0.5) %
4	H2O	natural abundance		90 (±0.5) %
5	sodium phosphate	natural abundance		10 (±0.2) mM
6	sodium azide	natural abundance		0.1 (±0.01) %
7	sodium chloride	natural abundance		100 (±1.0) mM
8	DTT	natural abundance		1 (±0.05) mM

6 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz TCI cryoprobes

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 (±0.1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-95% 15N]		0.5 (±0.05) mM
2	ZINC ION	natural abundance		0.5 (±0.05) mM
3	D2O	[U-99% 2H]		10 (±0.5) %
4	H2O	natural abundance		90 (±0.5) %
5	sodium phosphate	natural abundance		10 (±0.2) mM
6	sodium azide	natural abundance		0.1 (±0.01) %
7	sodium chloride	natural abundance		100 (±1.0) mM
8	DTT	natural abundance		1 (±0.05) mM

7 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz TCI cryoprobes

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.15 (±0.1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	entity_1	[U-95% 15N]		0.5 (±0.05) mM
2	ZINC ION	natural abundance		0.5 (±0.05) mM
3	D2O	[U-99% 2H]		10 (±0.5) %
4	H2O	natural abundance		90 (±0.5) %
5	sodium phosphate	natural abundance		10 (±0.2) mM
6	sodium azide	natural abundance		0.1 (±0.01) %
7	sodium chloride	natural abundance		100 (±1.0) mM
8	DTT	natural abundance		1 (±0.05) mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15926_2k7r.nef
Input source #2: Coordindates	2k7r.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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:67:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:70:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:84:HIS:NE2	2:1:ZN:ZN	unknown	unknown	n/a
1:101:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	ZN	ZINC ION	None

Sequence alignments

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

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
MEPIGRSLQGVTGRPDFQKRLEQMKEKVMKDQDVQAFLKENEEVIDQKMIEKSLNKLYEYIEQSKNCSYCSEDENCNNLLEGYHPKLVVNGRSIDIEYYE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MEPIGRSLQGVTGRPDFQKRLEQMKEKVMKDQDVQAFLKENEEVIDQKMIEKSLNKLYEYIEQSKNCSYCSEDENCNNLLEGYHPKLVVNGRSIDIEYYE

------
CPVKRK
||||||
CPVKRK

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	106	0	0	100.0

Content subtype: combined_15926_2k7r.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	791		100.0 (chain: A, length: 106)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	2901 (1)	noe	99.1 (chain: A, length: 106)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	Warning	523 (513)	.	100.0 (chain: A, length: 106)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 106, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 677
  - ¹⁵N chemical shifts: 114
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

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: 106, Sequence coverage: 99.1%
- Total number of restraints: 2894
- Weight of restraints: 1.0 (2894)
- Potential type of restraints: upper-bound-parabolic (2894)
- Range of distance target values: 2.37, 6.89 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 106, Sequence coverage: 100.0%
- Total number of restraints: 513
- Total number of restraints per polymer type: 513
- Weight of restraints: 1.0 (513)
- Potential type of restraints: square-well-parabolic (513)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords DnaI N-terminal domain, helicase-loading protein, NMR structure