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BMRB: 19317

2MA1

Solution structure of HRDC1 domain of RecQ helicase from Deinococcus radiodurans

Authors

Liu, S., Zhang, W., Gao, Z., Ming, Q., Hou, H., Lan, W., Wu, H., Cao, C., Dong, Y.

Assembly

DNA helicase RecQ

Entity

1. DNA helicase RecQ (polymer, Thiol state: not present), 75 monomers, 8042.041 Da Detail

HDAPLFEALR AWRLQKAKEL SLPPYTIFHD ATLKTIAELR PGSHATLGTV SGVGGRKLAA YGDEVLQVVR DSSGG

Formula weight

8042.041 Da

Source organism

Deinococcus radiodurans

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 92.2 %, Completeness (bb): 97.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.2 % (773 of 838)	96.1 % (414 of 431)	86.8 % (289 of 333)	94.6 % (70 of 74)
Backbone	97.3 % (430 of 442)	98.7 % (152 of 154)	96.3 % (209 of 217)	97.2 % (69 of 71)
Sidechain	88.6 % (410 of 463)	94.6 % (262 of 277)	80.3 % (147 of 183)	33.3 % (1 of 3)
Aromatic	70.0 % (42 of 60)	80.0 % (24 of 30)	62.1 % (18 of 29)	0.0 % (0 of 1)
Methyl	94.8 % (91 of 96)	100.0 % (48 of 48)	89.6 % (43 of 48)

1. DNA helicase RecQ

HDAPLFEALR AWRLQKAKEL SLPPYTIFHD ATLKTIAELR PGSHATLGTV SGVGGRKLAA YGDEVLQVVR DSSGG

Show sample condition

Sample

Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 293 K, pH 7.0, Details 50mM phosphate buffer; 90% H2O, 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	HRDC1	[U-98% 13C; U-98% 15N]		2 mM
2	phosphate buffer	natural abundance		50 mM

Protein Blocks Logo

Calculated from 1 models in PDB: 2MA1, Strand ID: A Detail

Release date

2013-07-07

Citation

NMR structure of the N-terminal-most HRDC1 domain of RecQ helicase from Deinococcus radiodurans
Liu, S., Zhang, W., Gao, Z., Ming, Q., Hou, H., Lan, W., Wu, H., Cao, C., Dong, Y.
FEBS Lett. (2013), 587, 2635-2642, PubMed 23831579 , DOI 10.1016/j.febslet.2013.06.048 , Abstract

Entries sharing articles BMRB: 1 entries Detail

BMRB: 18124 released on 2014-04-22
Title Solution Structure of D. radiodurans RecQ HRDC domain 1

Related entities 1. DNA helicase RecQ, : 1 : 40 entities Detail

Experiments performed 3 experiments Detail

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19317_2ma1.nef
Input source #2: Coordindates	2ma1.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

--540-------550-------560-------570-------580-------590-------600-------610
HDAPLFEALRAWRLQKAKELSLPPYTIFHDATLKTIAELRPGSHATLGTVSGVGGRKLAAYGDEVLQVVRDSSGG
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
HDAPLFEALRAWRLQKAKELSLPPYTIFHDATLKTIAELRPGSHATLGTVSGVGGRKLAAYGDEVLQVVRDSSGG
--------10--------20--------30--------40--------50--------60--------70-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	75	0	0	100.0

Content subtype: combined_19317_2ma1.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	768		100.0 (chain: A, length: 75)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	1640 (1)	noe	100.0 (chain: A, length: 75)
2	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	52 (1)	hbond	56.0 (chain: A, length: 75)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	94 (94)	.	78.7 (chain: A, length: 75)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 75, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 415
  - ¹³C chemical shifts: 283
  - ¹⁵N chemical shifts: 70
- Completeness of assignments
  - Entity_assemble_ID: A
- 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)
548	ARG	HH11	6.717
548	ARG	HH21	6.715
579	HIS	HD1	7.666

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	431	412	95.6
¹³C chemical shifts	333	283	85.0
¹⁵N chemical shifts	79	70	88.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	154	151	98.1
¹³C chemical shifts	150	142	94.7
¹⁵N chemical shifts	71	69	97.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	277	261	94.2
¹³C chemical shifts	183	141	77.0
¹⁵N chemical shifts	8	1	12.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	48	48	100.0
¹³C chemical shifts	48	41	85.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	30	24	80.0
¹³C chemical shifts	29	18	62.1
¹⁵N chemical shifts	1	0	0.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 75, Sequence coverage: 100.0%
- Total number of restraints: 1639
- Weight of restraints: 1.0 (1639)
- Potential type of restraints: square-well-parabolic (1639)
- Range of distance target values: 2.35, 10.3 (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
- Saveframe: CNS/XPLOR_distance_constraints_2
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 75, Sequence coverage: 56.0%
  - Total number of restraints: 52
  - Weight of restraints: 1.0 (52)
  - Potential type of restraints: square-well-parabolic (52)
  - Range of distance target values: 2.05, 2.85 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - 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: 75, Sequence coverage: 78.7%
- Total number of restraints: 94
- Total number of restraints per polymer type: 94
- Weight of restraints: 1.0 (94)
- Potential type of restraints: square-well-parabolic (94)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords DNA binding domain

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Found 1 Document (0.602 seconds)

BMRB: 19317

Sample

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. DNA helicase RecQ, : 1 : 40 entities Detail

Experiments performed 3 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail