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BMRB: 19986

2MPJ

NMR structure of Xenopus RecQ4 zinc knuckle

Authors

Zucchelli, C., Marino, F., Mojumdar, A., Onesti, S., Musco, G.

Assembly

Xenopus RecQ4 zinc knuckle

Entity

1. RecQ4 zinc knuckle (polymer, Thiol state: all other bound), 25 monomers, 2610.885 Da Detail

NRSGDTCFRC GGMGHWASQC PGSVP

2. ZINC ION (non-polymer), 65.409 Da

Total weight

2676.294 Da

Max. entity weight

2610.885 Da

Entity Connection

ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:CYS7:SG	2:ZN1:ZN
2	na	sing	1:CYS10:SG	2:ZN1:ZN
3	na	sing	1:CYS20:SG	2:ZN1:ZN

Source organism

Exptl. method

Refine. method

simulated annealing, molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 78.8 %, Completeness (bb): 80.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	78.8 % (201 of 255)	99.2 % (132 of 133)	50.0 % (48 of 96)	80.8 % (21 of 26)
Backbone	80.8 % (118 of 146)	98.1 % (52 of 53)	64.3 % (45 of 70)	91.3 % (21 of 23)
Sidechain	79.8 % (103 of 129)	100.0 % (80 of 80)	50.0 % (23 of 46)	0.0 % (0 of 3)
Aromatic	50.0 % (13 of 26)	100.0 % (13 of 13)	0.0 % (0 of 12)	0.0 % (0 of 1)
Methyl	75.0 % (6 of 8)	100.0 % (4 of 4)	50.0 % (2 of 4)

1. RecQ4 zinc knuckle

NRSGDTCFRC GGMGHWASQC PGSVP

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	RecQ4 zinc knuckle	natural abundance		1.1 mM
2	ZnCl2	natural abundance		1.25 mM
3	D2O	[U-100% 2H]		10 %
4	sodium phosphate pH 6.3	natural abundance		20 mM
5	potassium chloride	natural abundance		150 mM
6	DTT	natural abundance		4 mM
7	DSS	natural abundance		0.3 mM
8	H2O	natural abundance		90 %

Protein Blocks Logo

Calculated from 15 models in PDB: 2MPJ, Strand ID: A Detail

Release date

2015-08-02

Citation

Structural and biochemical characterization of an RNA/DNA binding motif in the N-terminal domain of RecQ4 helicases
Marino, F., Mojumdar, A., Zucchelli, C., Musco, G., Buratti, E., Vindigni, A., Onesti, S.
Sci. Rep. (2016), 6, 21501-21501, PubMed 26888063 , DOI 10.1038/srep21501 , Abstract

Related entities 1. RecQ4 zinc knuckle, : 1 : 50 entities Detail

Experiments performed 5 experiments Detail

1 1D 1H

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	RecQ4 zinc knuckle	natural abundance		1.1 mM
2	ZnCl2	natural abundance		1.25 mM
3	D2O	[U-100% 2H]		10 %
4	sodium phosphate pH 6.3	natural abundance		20 mM
5	potassium chloride	natural abundance		150 mM
6	DTT	natural abundance		4 mM
7	DSS	natural abundance		0.3 mM
8	H2O	natural abundance		90 %

2 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	RecQ4 zinc knuckle	natural abundance		1.1 mM
2	ZnCl2	natural abundance		1.25 mM
3	D2O	[U-100% 2H]		10 %
4	sodium phosphate pH 6.3	natural abundance		20 mM
5	potassium chloride	natural abundance		150 mM
6	DTT	natural abundance		4 mM
7	DSS	natural abundance		0.3 mM
8	H2O	natural abundance		90 %

3 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	RecQ4 zinc knuckle	natural abundance		1.1 mM
2	ZnCl2	natural abundance		1.25 mM
3	D2O	[U-100% 2H]		10 %
4	sodium phosphate pH 6.3	natural abundance		20 mM
5	potassium chloride	natural abundance		150 mM
6	DTT	natural abundance		4 mM
7	DSS	natural abundance		0.3 mM
8	H2O	natural abundance		90 %

4 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	RecQ4 zinc knuckle	natural abundance		1.1 mM
2	ZnCl2	natural abundance		1.25 mM
3	D2O	[U-100% 2H]		10 %
4	sodium phosphate pH 6.3	natural abundance		20 mM
5	potassium chloride	natural abundance		150 mM
6	DTT	natural abundance		4 mM
7	DSS	natural abundance		0.3 mM
8	H2O	natural abundance		90 %

5 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	RecQ4 zinc knuckle	natural abundance		1.1 mM
2	ZnCl2	natural abundance		1.25 mM
3	D2O	[U-100% 2H]		10 %
4	sodium phosphate pH 6.3	natural abundance		20 mM
5	potassium chloride	natural abundance		150 mM
6	DTT	natural abundance		4 mM
7	DSS	natural abundance		0.3 mM
8	H2O	natural abundance		90 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_19986_2mpj.nef
Input source #2: Coordindates	2mpj.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)
1:15:HIS:NE2	2:1:ZN:ZN	unknown	unknown	n/a
1:7:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:20:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:10: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-----
NRSGDTCFRCGGMGHWASQCPGSVP
|||||||||||||||||||||||||
NRSGDTCFRCGGMGHWASQCPGSVP

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	25	0	0	100.0

Content subtype: combined_19986_2mpj.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	OK	196		100.0 (chain: A, length: 25)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	197 (1)	noe	100.0 (chain: A, length: 25)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	3 (1)	hbond	16.0 (chain: A, length: 25)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 25, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 132
  - ¹³C chemical shifts: 43
  - ¹⁵N chemical shifts: 21
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- 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: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 25, Sequence coverage: 100.0%
- Total number of restraints: 196
- Weight of restraints: 1.0 (196)
- Potential type of restraints: square-well-parabolic (196)
- Range of distance target values: 1.56, 4.89 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 25, Sequence coverage: 16.0%
  - Total number of restraints: 3
  - Weight of restraints: 1.0 (3)
  - Potential type of restraints: square-well-parabolic (3)
  - Range of distance target values: 2.21, 2.21 (Å)
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map

Keywords DNA/RNA binding, RecQ4, helicase, protein, zinc knuckle