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Found 1 Document (1.201 seconds)

BMRB: 17324

2MC3

NMR Solution Structure of the winged-helix domain from MUS81 junction-specific endonuclease

Authors

Harris, R., Fadden, A., McDonald, N.Q.

Assembly

Mus81-winged helix domain

Entity

1. Mus81-winged helix domain (polymer, Thiol state: all free), 103 monomers, 11458.06 Da Detail

GSYWPARHSG ARVILLVLYR EHLNPNGHHF LTKEELLQRC AQKSPRVAPG SAPPWPALRS LLHRNLVLRT HQPARYSLTP EGLELAQKLA ESEGLSLLNV GIG

Formula weight

11458.06 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

SIMULATED ANNEALING, SIMULATED ANNEALING

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 93.5 %, Completeness (bb): 92.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	93.5 % (1130 of 1208)	94.8 % (599 of 632)	92.6 % (437 of 472)	90.4 % (94 of 104)
Backbone	92.7 % (556 of 600)	93.7 % (192 of 205)	93.0 % (280 of 301)	89.4 % (84 of 94)
Sidechain	95.2 % (669 of 703)	95.3 % (407 of 427)	94.7 % (252 of 266)	100.0 % (10 of 10)
Aromatic	81.7 % (67 of 82)	87.8 % (36 of 41)	74.4 % (29 of 39)	100.0 % (2 of 2)
Methyl	99.2 % (127 of 128)	98.4 % (63 of 64)	100.0 % (64 of 64)

1. Mus81-winged helix domain

GSYWPARHSG ARVILLVLYR EHLNPNGHHF LTKEELLQRC AQKSPRVAPG SAPPWPALRS LLHRNLVLRT HQPARYSLTP EGLELAQKLA ESEGLSLLNV GIG

Show sample condition

Sample #1

Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 25mM Na phosphate buffer; 250mM NaCl; 1mM EDTA; 1mM DTT; pH 7.0

#	Name	Isotope labeling	Concentration
1	Mus81-winged helix domain	[U-100% 13C; U-100% 15N]	1 mM
2	sodium phosphate	natural abundance	25 mM
3	sodium chloride	natural abundance	250 mM
4	EDTA	natural abundance	1 mM
5	DTT	natural abundance	1 mM
6	D2O	natural abundance	10 %
7	H2O	natural abundance	90 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 25mM Na phosphate buffer; 250mM NaCl; 1mM EDTA; 1mM DTT; pH 7.0

#	Name	Isotope labeling	Concentration
8	Mus81-winged helix domain	[U-100% 13C; U-100% 15N]	1 mM
9	sodium phosphate	natural abundance	25 mM
10	sodium chloride	natural abundance	250 mM
11	EDTA	natural abundance	1 mM
12	DTT	natural abundance	1 mM
13	D2O	natural abundance	100 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 25mM Na phosphate buffer; 250mM NaCl; 1mM EDTA; 1mM DTT; pH 7.0; 5% n-octyl-penta(ethyleneglycol):octanol 0.96:1

#	Name	Isotope labeling	Concentration
14	Mus81-winged helix domain	[U-100% 15N]	1 mM
15	sodium phosphate	natural abundance	25 mM
16	sodium chloride	natural abundance	250 mM
17	EDTA	natural abundance	1 mM
18	DTT	natural abundance	1 mM
19	n-octyl-penta(ethyleneglycol):octanol 0.96:1	natural abundance	5 %
20	D2O	natural abundance	10 %
21	H2O	natural abundance	90 %

Sample #4

Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 25mM Na phosphate buffer; 250mM NaCl; 1mM EDTA; 1mM DTT; pH 7.0

#	Name	Isotope labeling	Concentration
22	Mus81-winged helix domain	[U-100% 15N]	1 mM
23	sodium phosphate	natural abundance	25 mM
24	sodium chloride	natural abundance	250 mM
25	EDTA	natural abundance	1 mM
26	DTT	natural abundance	1 mM
27	D2O	natural abundance	10 %
28	H2O	natural abundance	90 %

LACS Plot; CA

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

Referencing offset: -0.21 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: -0.21 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: 0.05 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: -0.14 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2MC3, Strand ID: A Detail

Release date

2013-09-15

Related entities 1. Mus81-winged helix domain, : 1 : 2 : 24 entities Detail

Interaction partners 1. Mus81-winged helix domain, : 16 interactors Detail

More details for 16 interactors identified by 6 citations

Experiments performed 8 experiments Detail

1 3D 15N NOESY-HSQC

Instrument

Varian UnityPlus - 500 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 25mM Na phosphate buffer; 250mM NaCl; 1mM EDTA; 1mM DTT; pH 7.0

#	Name	Isotope labeling	Concentration
22	Mus81-winged helix domain	[U-100% 15N]	1 mM
23	sodium phosphate	natural abundance	25 mM
24	sodium chloride	natural abundance	250 mM
25	EDTA	natural abundance	1 mM
26	DTT	natural abundance	1 mM
27	D2O	natural abundance	10 %
28	H2O	natural abundance	90 %

2 3D 13C NOESY-HSQC

Instrument

Varian UnityPlus - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 25mM Na phosphate buffer; 250mM NaCl; 1mM EDTA; 1mM DTT; pH 7.0

#	Name	Isotope labeling	Concentration
8	Mus81-winged helix domain	[U-100% 13C; U-100% 15N]	1 mM
9	sodium phosphate	natural abundance	25 mM
10	sodium chloride	natural abundance	250 mM
11	EDTA	natural abundance	1 mM
12	DTT	natural abundance	1 mM
13	D2O	natural abundance	100 %

3 3D 13C aromatic NOESY-HSQC

Instrument

Varian UnityPlus - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 25mM Na phosphate buffer; 250mM NaCl; 1mM EDTA; 1mM DTT; pH 7.0

#	Name	Isotope labeling	Concentration
8	Mus81-winged helix domain	[U-100% 13C; U-100% 15N]	1 mM
9	sodium phosphate	natural abundance	25 mM
10	sodium chloride	natural abundance	250 mM
11	EDTA	natural abundance	1 mM
12	DTT	natural abundance	1 mM
13	D2O	natural abundance	100 %

4 2D IPAP

Instrument

Varian UnityPlus - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 25mM Na phosphate buffer; 250mM NaCl; 1mM EDTA; 1mM DTT; pH 7.0; 5% n-octyl-penta(ethyleneglycol):octanol 0.96:1

#	Name	Isotope labeling	Concentration
14	Mus81-winged helix domain	[U-100% 15N]	1 mM
15	sodium phosphate	natural abundance	25 mM
16	sodium chloride	natural abundance	250 mM
17	EDTA	natural abundance	1 mM
18	DTT	natural abundance	1 mM
19	n-octyl-penta(ethyleneglycol):octanol 0.96:1	natural abundance	5 %
20	D2O	natural abundance	10 %
21	H2O	natural abundance	90 %

5 2D 1H-15N HSQC

Instrument

Varian UnityPlus - 500 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 25mM Na phosphate buffer; 250mM NaCl; 1mM EDTA; 1mM DTT; pH 7.0

#	Name	Isotope labeling	Concentration
22	Mus81-winged helix domain	[U-100% 15N]	1 mM
23	sodium phosphate	natural abundance	25 mM
24	sodium chloride	natural abundance	250 mM
25	EDTA	natural abundance	1 mM
26	DTT	natural abundance	1 mM
27	D2O	natural abundance	10 %
28	H2O	natural abundance	90 %

6 2D 1H-13C HSQC

Instrument

Varian UnityPlus - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 25mM Na phosphate buffer; 250mM NaCl; 1mM EDTA; 1mM DTT; pH 7.0

#	Name	Isotope labeling	Concentration
8	Mus81-winged helix domain	[U-100% 13C; U-100% 15N]	1 mM
9	sodium phosphate	natural abundance	25 mM
10	sodium chloride	natural abundance	250 mM
11	EDTA	natural abundance	1 mM
12	DTT	natural abundance	1 mM
13	D2O	natural abundance	100 %

7 3D HNCO

Instrument

Varian UnityPlus - 500 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 25mM Na phosphate buffer; 250mM NaCl; 1mM EDTA; 1mM DTT; pH 7.0

#	Name	Isotope labeling	Concentration
1	Mus81-winged helix domain	[U-100% 13C; U-100% 15N]	1 mM
2	sodium phosphate	natural abundance	25 mM
3	sodium chloride	natural abundance	250 mM
4	EDTA	natural abundance	1 mM
5	DTT	natural abundance	1 mM
6	D2O	natural abundance	10 %
7	H2O	natural abundance	90 %

8 2D 1H-13C aromatic HSQC

Instrument

Varian UnityPlus - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 25mM Na phosphate buffer; 250mM NaCl; 1mM EDTA; 1mM DTT; pH 7.0

#	Name	Isotope labeling	Concentration
8	Mus81-winged helix domain	[U-100% 13C; U-100% 15N]	1 mM
9	sodium phosphate	natural abundance	25 mM
10	sodium chloride	natural abundance	250 mM
11	EDTA	natural abundance	1 mM
12	DTT	natural abundance	1 mM
13	D2O	natural abundance	100 %

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_17324_2mc3.nef
Input source #2: Coordindates	2mc3.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

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

---100---
LSLLNVGIG
|||||||||
LSLLNVGIG
---------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	109	0	0	100.0

Content subtype: combined_17324_2mc3.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1121		94.5 (chain: A, length: 109)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1911 (1)	noe	91.7 (chain: A, length: 109)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	21 (1)	noe	16.5 (chain: A, length: 109)
3	Distance restraints	CNS/XPLOR_distance_constraints_5	Warning	38 (1)	hbond	26.6 (chain: A, length: 109)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	110 (110)	.	60.6 (chain: A, length: 109)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_6	OK	71 (71)	.	65.1 (chain: A, length: 109)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 109, Sequence coverage: 94.5%
- Total number of assignments
  - ¹H chemical shifts: 599
  - ¹³C chemical shifts: 432
  - ¹⁵N chemical shifts: 90
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	660	599	90.8
¹³C chemical shifts	493	432	87.6
¹⁵N chemical shifts	118	90	76.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	218	191	87.6
¹³C chemical shifts	218	182	83.5
¹⁵N chemical shifts	99	80	80.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	442	408	92.3
¹³C chemical shifts	275	250	90.9
¹⁵N chemical shifts	19	10	52.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	66	64	97.0
¹³C chemical shifts	66	64	97.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	41	36	87.8
¹³C chemical shifts	39	28	71.8
¹⁵N chemical shifts	2	2	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 109, Sequence coverage: 91.7%
- Total number of restraints: 1907
- Weight of restraints: 1.0 (1907)
- Potential type of restraints: square-well-parabolic (1907)
- Range of distance target values: 2.4, 3.9 (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_3
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 109, Sequence coverage: 16.5%
  - Total number of restraints: 21
  - Weight of restraints: 1.0 (21)
  - Potential type of restraints: square-well-parabolic (21)
  - Range of distance target values: 2.9, 3.65 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_5
    - Status: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 109, Sequence coverage: 26.6%
    - Total number of restraints: 38
    - Weight of restraints: 1.0 (38)
    - Potential type of restraints: square-well-parabolic (38)
    - Range of distance target values: 2.05, 3.05 (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_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 109, Sequence coverage: 60.6%
- Total number of restraints: 110
- Total number of restraints per polymer type: 110
- Weight of restraints: 1.0 (110)
- Potential type of restraints: square-well-parabolic (110)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_6

Status: OK
Experiment type: .

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 109, Sequence coverage: 65.1%

--------------10--------20--------30--------40--------50--------60--------70--------80--------90----
GPTMGSGSYWPARHSGARVILLVLYREHLNPNGHHFLTKEELLQRCAQKSPRVAPGSAPPWPALRSLLHRNLVLRTHQPARYSLTPEGLELAQKLAESEG
         | |    |||||||||||||| ||| |||||||||||||   | |          |||||||||||||| |||||| ||||||||||||||
.........W.A....ARVILLVLYREHLN.NGH.FLTKEELLQRCAQ...R.A..........RSLLHRNLVLRTHQ.ARYSLT.EGLELAQKLAESEG
--------------10--------20--------30--------40--------50--------60--------70--------80--------90----

---100---
LSLLNVGIG
|||      
LSL      
---

Total number of restraints: 71
Potential type of restraints: undefined (71)
Range of observed RDC values: 100.0, -100.0 (Hz)
RDC restraints per residue
- Chain_ID: A
  None

Keywords alpha beta, winged-helix

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Found 1 Document (1.201 seconds)

BMRB: 17324

Sample #1

Sample #2

Sample #3

Sample #4

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Mus81-winged helix domain, : 1 : 2 : 24 entities Detail

Interaction partners 1. Mus81-winged helix domain, : 16 interactors Detail

Experiments performed 8 experiments Detail

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NMR combined restraints 7 contents Detail