BMRBj - BMREntryMaster

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BMRB: 34122

5NOC

Solution NMR Structure of the C-terminal domain of ParB (Spo0J)

Authors

Higman, V.A., Fisher, G.L.M., Dillingham, M.S., Crump, M.P.

Assembly

Stage 0 sporulation protein J

Entity

1. Stage 0 sporulation protein J (polymer, Thiol state: not present), 69 monomers, 8096.079 × 2 Da Detail

GPGQNVPRET KKKEPVKDAV LKERESYLQN YFGTTVNIKR QKKKGKIEIE FFSNEDLDRI LELLSERES

Total weight

16192.158 Da

Max. entity weight

8096.079 Da

Source organism

Bacillus subtilis

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.6 %, Completeness: 94.9 %, Completeness (bb): 95.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	94.9 % (817 of 861)	94.2 % (435 of 462)	95.4 % (311 of 326)	97.3 % (71 of 73)
Backbone	95.6 % (390 of 408)	94.2 % (131 of 139)	96.1 % (195 of 203)	97.0 % (64 of 66)
Sidechain	95.0 % (492 of 518)	94.1 % (304 of 323)	96.3 % (181 of 188)	100.0 % (7 of 7)
Aromatic	82.6 % (38 of 46)	82.6 % (19 of 23)	82.6 % (19 of 23)
Methyl	96.9 % (62 of 64)	93.8 % (30 of 32)	100.0 % (32 of 32)

1. entity 1

GPGQNVPRET KKKEPVKDAV LKERESYLQN YFGTTVNIKR QKKKGKIEIE FFSNEDLDRI LELLSERES

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 208 K, pH 6.1, Details 3 mM ParB (Spo0J), 137 mM sodium chloride, 2.7 mM potassium chloride, 10 mM Na2HPO4, 1.8 mM KH2PO4, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	ParB (Spo0J)	natural abundance	3 mM
2	sodium chloride	natural abundance	137 mM
3	potassium chloride	natural abundance	2.7 mM
4	Na2HPO4	natural abundance	10 mM
5	KH2PO4	natural abundance	1.8 mM

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 208 K, pH 6.1, Details 3 mM [U-13C; U-15N] ParB (Spo0J), 137 mM sodium chloride, 2.7 mM potassium chloride, 10 mM Na2HPO4, 1.8 mM KH2PO4, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
6	ParB (Spo0J)	[U-13C; U-15N]	3 mM
7	sodium chloride	natural abundance	137 mM
8	potassium chloride	natural abundance	2.7 mM
9	Na2HPO4	natural abundance	10 mM
10	KH2PO4	natural abundance	1.8 mM

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 208 K, pH 6.1, Details 1.5 mM ParB (Spo0J), 1.5 mM [U-13C; U-15N] ParB (Spo0J), 137 mM sodium chloride, 2.7 mM potassium chloride, 10 mM Na2HPO4, 1.8 mM KH2PO4, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
11	ParB (Spo0J)	natural abundance	1.5 mM
12	sodium chloride	natural abundance	137 mM
13	potassium chloride	natural abundance	2.7 mM
14	Na2HPO4	natural abundance	10 mM
15	KH2PO4	natural abundance	1.8 mM
16	ParB (Spo0J)-label	[U-13C; U-15N]	1.5 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.2514495
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: -0.39 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.2514495
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: -0.39 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.2514495
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: -0.03 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.2514495
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: 0.06 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 5NOC, Strand ID: A, B Detail

Release date

2017-12-07

Citation

The structural basis for dynamic DNA binding and bridging interactions which condense the bacterial centromere
Fisher, G.L.M., Pastrana, C.L., Higman, V.A., Koh, A., Taylor, J.A., Butterer, A., Craggs, T.D., Sobott, F., Murray, H., Crump, M.P., Moreno-Herrero, F., Dillingham, M.S.
Elife (2017), 6, e28086-e28086, PubMed 29244022 , DOI 10.7554/eLife.28086 , Abstract

Related entities 1. Stage 0 sporulation protein J, : 1 : 1 : 31 entities Detail

Interaction partners 1. Stage 0 sporulation protein J, : 4 interactors Detail

More details for 4 interactors identified by 3 citations

Experiments performed 17 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian VNMRS - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 208 K, pH 6.1, Details 3 mM [U-13C; U-15N] ParB (Spo0J), 137 mM sodium chloride, 2.7 mM potassium chloride, 10 mM Na2HPO4, 1.8 mM KH2PO4, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
6	ParB (Spo0J)	[U-13C; U-15N]	3 mM
7	sodium chloride	natural abundance	137 mM
8	potassium chloride	natural abundance	2.7 mM
9	Na2HPO4	natural abundance	10 mM
10	KH2PO4	natural abundance	1.8 mM

2 2D 1H-13C HSQC

Instrument

Varian VNMRS - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	ParB (Spo0J)	[U-13C; U-15N]	3 mM
7	sodium chloride	natural abundance	137 mM
8	potassium chloride	natural abundance	2.7 mM
9	Na2HPO4	natural abundance	10 mM
10	KH2PO4	natural abundance	1.8 mM

3 3D HNCO

Instrument

Varian VNMRS - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	ParB (Spo0J)	[U-13C; U-15N]	3 mM
7	sodium chloride	natural abundance	137 mM
8	potassium chloride	natural abundance	2.7 mM
9	Na2HPO4	natural abundance	10 mM
10	KH2PO4	natural abundance	1.8 mM

4 3D HNCA

Instrument

Varian VNMRS - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	ParB (Spo0J)	[U-13C; U-15N]	3 mM
7	sodium chloride	natural abundance	137 mM
8	potassium chloride	natural abundance	2.7 mM
9	Na2HPO4	natural abundance	10 mM
10	KH2PO4	natural abundance	1.8 mM

5 3D HN(CO)CA

Instrument

Varian VNMRS - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	ParB (Spo0J)	[U-13C; U-15N]	3 mM
7	sodium chloride	natural abundance	137 mM
8	potassium chloride	natural abundance	2.7 mM
9	Na2HPO4	natural abundance	10 mM
10	KH2PO4	natural abundance	1.8 mM

6 3D HNCACB

Instrument

Varian VNMRS - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	ParB (Spo0J)	[U-13C; U-15N]	3 mM
7	sodium chloride	natural abundance	137 mM
8	potassium chloride	natural abundance	2.7 mM
9	Na2HPO4	natural abundance	10 mM
10	KH2PO4	natural abundance	1.8 mM

7 3D CBCA(CO)NH

Instrument

Varian VNMRS - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	ParB (Spo0J)	[U-13C; U-15N]	3 mM
7	sodium chloride	natural abundance	137 mM
8	potassium chloride	natural abundance	2.7 mM
9	Na2HPO4	natural abundance	10 mM
10	KH2PO4	natural abundance	1.8 mM

8 3D C(CO)NH

Instrument

Varian VNMRS - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	ParB (Spo0J)	[U-13C; U-15N]	3 mM
7	sodium chloride	natural abundance	137 mM
8	potassium chloride	natural abundance	2.7 mM
9	Na2HPO4	natural abundance	10 mM
10	KH2PO4	natural abundance	1.8 mM

9 3D H(CCO)NH

Instrument

Varian VNMRS - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	ParB (Spo0J)	[U-13C; U-15N]	3 mM
7	sodium chloride	natural abundance	137 mM
8	potassium chloride	natural abundance	2.7 mM
9	Na2HPO4	natural abundance	10 mM
10	KH2PO4	natural abundance	1.8 mM

10 3D HCCH-TOCSY

Instrument

Varian VNMRS - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	ParB (Spo0J)	[U-13C; U-15N]	3 mM
7	sodium chloride	natural abundance	137 mM
8	potassium chloride	natural abundance	2.7 mM
9	Na2HPO4	natural abundance	10 mM
10	KH2PO4	natural abundance	1.8 mM

11 3D 1H-15N NOESY

Instrument

Varian VNMRS - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	ParB (Spo0J)	[U-13C; U-15N]	3 mM
7	sodium chloride	natural abundance	137 mM
8	potassium chloride	natural abundance	2.7 mM
9	Na2HPO4	natural abundance	10 mM
10	KH2PO4	natural abundance	1.8 mM

12 3D 1H-13C NOESY aliphatic

Instrument

Varian VNMRS - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	ParB (Spo0J)	[U-13C; U-15N]	3 mM
7	sodium chloride	natural abundance	137 mM
8	potassium chloride	natural abundance	2.7 mM
9	Na2HPO4	natural abundance	10 mM
10	KH2PO4	natural abundance	1.8 mM

13 3D 1H-13C NOESY aromatic

Instrument

Varian VNMRS - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
6	ParB (Spo0J)	[U-13C; U-15N]	3 mM
7	sodium chloride	natural abundance	137 mM
8	potassium chloride	natural abundance	2.7 mM
9	Na2HPO4	natural abundance	10 mM
10	KH2PO4	natural abundance	1.8 mM

14 2D 1H-1H TOCSY

Instrument

Varian VNMRS - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 208 K, pH 6.1, Details 3 mM ParB (Spo0J), 137 mM sodium chloride, 2.7 mM potassium chloride, 10 mM Na2HPO4, 1.8 mM KH2PO4, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	ParB (Spo0J)	natural abundance	3 mM
2	sodium chloride	natural abundance	137 mM
3	potassium chloride	natural abundance	2.7 mM
4	Na2HPO4	natural abundance	10 mM
5	KH2PO4	natural abundance	1.8 mM

15 2D 1H-1H NOESY

Instrument

Varian VNMRS - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	ParB (Spo0J)	natural abundance	3 mM
2	sodium chloride	natural abundance	137 mM
3	potassium chloride	natural abundance	2.7 mM
4	Na2HPO4	natural abundance	10 mM
5	KH2PO4	natural abundance	1.8 mM

16 3D 13C,15N F1-filtered, 13C,15N F3-edited 13C-NOSEY-HSQC

Instrument

Varian VNMRS - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 208 K, pH 6.1, Details 1.5 mM ParB (Spo0J), 1.5 mM [U-13C; U-15N] ParB (Spo0J), 137 mM sodium chloride, 2.7 mM potassium chloride, 10 mM Na2HPO4, 1.8 mM KH2PO4, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
11	ParB (Spo0J)	natural abundance	1.5 mM
12	sodium chloride	natural abundance	137 mM
13	potassium chloride	natural abundance	2.7 mM
14	Na2HPO4	natural abundance	10 mM
15	KH2PO4	natural abundance	1.8 mM
16	ParB (Spo0J)-label	[U-13C; U-15N]	1.5 mM

17 3D 13C,15N F1-filtered, 13C,15N F3-edited 15N-NOSEY-HSQC

Instrument

Varian VNMRS - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
11	ParB (Spo0J)	natural abundance	1.5 mM
12	sodium chloride	natural abundance	137 mM
13	potassium chloride	natural abundance	2.7 mM
14	Na2HPO4	natural abundance	10 mM
15	KH2PO4	natural abundance	1.8 mM
16	ParB (Spo0J)-label	[U-13C; U-15N]	1.5 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_34122_5noc.nef
Input source #2: Coordindates	5noc.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

----220-------230-------240-------250-------260-------270-------280--
GPGQNVPRETKKKEPVKDAVLKERESYLQNYFGTTVNIKRQKKKGKIEIEFFSNEDLDRILELLSERES
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GPGQNVPRETKKKEPVKDAVLKERESYLQNYFGTTVNIKRQKKKGKIEIEFFSNEDLDRILELLSERES
--------10--------20--------30--------40--------50--------60---------

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

----220-------230-------240-------250-------260-------270-------280--
GPGQNVPRETKKKEPVKDAVLKERESYLQNYFGTTVNIKRQKKKGKIEIEFFSNEDLDRILELLSERES
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GPGQNVPRETKKKEPVKDAVLKERESYLQNYFGTTVNIKRQKKKGKIEIEFFSNEDLDRILELLSERES
--------10--------20--------30--------40--------50--------60---------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	69	0	0	100.0
B	B	69	0	0	100.0

Content subtype: combined_34122_5noc.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1694		98.6 (chain: A, length: 69), 98.6 (chain: B, length: 69)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	5606 (1)	noe	78.3 (chain: A, length: 69), 78.3 (chain: B, length: 69)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	56 (1)	hbond	53.6 (chain: A, length: 69), 53.6 (chain: B, length: 69)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	160 (160)	.	66.7 (chain: A, length: 69), 66.7 (chain: B, length: 69)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 69, Sequence coverage: 98.6%
  - Entity_assembly_ID: B, Chain length: 69, Sequence coverage: 98.6%
- Total number of assignments
  - ¹H chemical shifts: 902
  - ¹³C chemical shifts: 642
  - ¹⁵N chemical shifts: 150
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- 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
  - Chain_ID: B

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
217	GLN	CD	180.587
218	ASN	CG	177.134
237	ARG	HH11	6.679
237	ARG	HH12	6.679
237	ARG	NH1	72.729
242	GLN	CD	180.392
243	ASN	CG	176.419
250	ASN	CG	175.93
254	GLN	CD	180.406
267	ASN	CG	176.119

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	462	449	97.2
¹³C chemical shifts	326	314	96.3
¹⁵N chemical shifts	78	74	94.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	139	134	96.4
¹³C chemical shifts	138	132	95.7
¹⁵N chemical shifts	66	64	97.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	323	315	97.5
¹³C chemical shifts	188	182	96.8
¹⁵N chemical shifts	12	10	83.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	32	32	100.0
¹³C chemical shifts	32	32	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	23	19	82.6
¹³C chemical shifts	23	19	82.6

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
217	GLN	CD	180.587
218	ASN	CG	177.134
237	ARG	HH11	6.679
237	ARG	HH12	6.679
237	ARG	NH1	72.729
242	GLN	CD	180.392
243	ASN	CG	176.419
250	ASN	CG	175.93
254	GLN	CD	180.406
267	ASN	CG	176.119

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	462	449	97.2
¹³C chemical shifts	326	314	96.3
¹⁵N chemical shifts	78	74	94.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	139	134	96.4
¹³C chemical shifts	138	132	95.7
¹⁵N chemical shifts	66	64	97.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	323	315	97.5
¹³C chemical shifts	188	182	96.8
¹⁵N chemical shifts	12	10	83.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	32	32	100.0
¹³C chemical shifts	32	32	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	23	19	82.6
¹³C chemical shifts	23	19	82.6

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 69, Sequence coverage: 78.3%
  - Entity_assembly_ID: B, Chain length: 69, Sequence coverage: 78.3%
- Total number of restraints: 5504
- Weight of restraints: 1.0 (5504)
- Potential type of restraints: square-well-parabolic (5504)
- Range of distance target values: 1.48, 7.78 (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: 69, Sequence coverage: 53.6%
    - Entity_assembly_ID: B, Chain length: 69, Sequence coverage: 53.6%
  - Total number of restraints: 56
  - Weight of restraints: 1.0 (56)
  - Potential type of restraints: square-well-parabolic (56)
  - Range of distance target values: 2.21, 2.21 (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: 69, Sequence coverage: 66.7%
  - Entity_assembly_ID: B, Chain length: 69, Sequence coverage: 66.7%
- Total number of restraints: 160
- Total number of restraints per polymer type: 160
- Weight of restraints: 1.0 (160)
- Potential type of restraints: square-well-parabolic (160)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

Keywords DNA binding protein, bacterial, centromere, chromosome, homodimer, segregation

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Found 1 Document (0.946 seconds)

BMRB: 34122

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Stage 0 sporulation protein J, : 1 : 1 : 31 entities Detail

Interaction partners 1. Stage 0 sporulation protein J, : 4 interactors Detail

Experiments performed 17 experiments Detail

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NMR combined restraints 5 contents Detail