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Found 1 Document (0.329 seconds)

BMRB: 30310

5W8Z

Solution Structure of XPH2, a Hybrid Sequence of Xfaso 1 and Pfl 6, Two Cro Proteins With Different Folds

Authors

Kumirov, V.K., Dykstra, E.M., Cordes, M.H.

Assembly

XPH2

Entity

1. XPH2 (polymer, Thiol state: all free), 70 monomers, 7872.872 Da Detail

MKKIPLSKYL EEHGTQSALA AALGVNQSAI SQMVRAGRCI DIELYTDGRV ECRELRPDVF GALEHHHHHH

Formula weight

7872.872 Da

Source organism

Pseudomonas fluorescens PF5

Exptl. method

solution NMR

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 90.0 %, Completeness: 79.3 %, Completeness (bb): 87.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	79.3 % (631 of 796)	81.4 % (336 of 413)	74.6 % (232 of 311)	87.5 % (63 of 72)
Backbone	87.3 % (363 of 416)	86.7 % (124 of 143)	87.8 % (180 of 205)	86.8 % (59 of 68)
Sidechain	73.3 % (326 of 445)	78.5 % (212 of 270)	64.3 % (110 of 171)	100.0 % (4 of 4)
Aromatic	25.9 % (14 of 54)	44.4 % (12 of 27)	7.4 % (2 of 27)
Methyl	94.9 % (74 of 78)	94.9 % (37 of 39)	94.9 % (37 of 39)

1. entity 1

MKKIPLSKYL EEHGTQSALA AALGVNQSAI SQMVRAGRCI DIELYTDGRV ECRELRPDVF GALEHHHHHH

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details 0.8 mM [U-13C; U-15N] XPH2, 50 mM NA- potassium phosphate, 150 mM NA- potassium chloride, 0.01 % NA- sodium azide, 0.1 mM NA- DSS, 1 M [U-2H] trimethylamine oxide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	DSS	natural abundance	0.1 mM
2	XPH2	[U-13C; U-15N]	0.8 mM
3	potassium chloride	natural abundance	150 mM
4	potassium phosphate	natural abundance	50 mM
5	sodium azide	natural abundance	0.01 %
6	trimethylamine oxide	[U-2H]	1 M

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details 0.6 mM [U-13C; U-15N] XPH2, 50 mM NA- potassium phosphate, 150 mM NA- potassium chloride, 0.01 % NA- sodium azide, 0.1 mM NA- DSS, 1 M [U-2H] trimethylamine oxide, 100% D2O

#	Name	Isotope labeling	Concentration
7	DSS	natural abundance	0.1 mM
8	XPH2	[U-13C; U-15N]	0.6 mM
9	potassium chloride	natural abundance	150 mM
10	potassium phosphate	natural abundance	50 mM
11	sodium azide	natural abundance	0.01 %
12	trimethylamine oxide	[U-2H]	1 M

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details 0.9 mM [U-15N] XPH2, 50 mM NA- potassium phosphate, 150 mM NA- potassium chloride, 0.01 % NA- sodium azide, 0.1 mM NA- DSS, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
13	DSS	natural abundance	0.1 mM
14	XPH2	[U-15N]	0.9 mM
15	potassium chloride	natural abundance	150 mM
16	potassium phosphate	natural abundance	50 mM
17	sodium azide	natural abundance	0.01 %

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details 1.6 mM [U-10% 13C] XPH2, 50 mM NA- potassium phosphate, 150 mM NA- potassium chloride, 0.01 % NA- sodium azide, 0.1 mM NA- DSS, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
18	DSS	natural abundance	0.1 mM
19	XPH2	[U-10% 13C]	1.6 mM
20	potassium chloride	natural abundance	150 mM
21	potassium phosphate	natural abundance	50 mM
22	sodium azide	natural abundance	0.01 %

LACS Plot; CA

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

Referencing offset: -0.2 ppm, Outliers: 3 Detail

LACS Plot; CB

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

Referencing offset: -0.2 ppm, Outliers: 3 Detail

LACS Plot; HA

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

Referencing offset: -0.19 ppm, Outliers: 1 Detail

Release date

2017-08-13

Citation

Multistep mutational transformation of a protein fold through structural intermediates
Kumirov, V.K., Dykstra, E.M., Hall, B.M., Anderson, W.J., Szyszka, T.N., Cordes, M.H.
Protein Sci. (2018), 27, 1767-1779, PubMed 30051937 , DOI 10.1002/pro.3488 , Abstract

Related entities 1. XPH2, : 1 : 14 entities Detail

Experiments performed 8 experiments Detail

1 3D_15N-separated_NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details 0.9 mM [U-15N] XPH2, 50 mM NA- potassium phosphate, 150 mM NA- potassium chloride, 0.01 % NA- sodium azide, 0.1 mM NA- DSS, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
13	DSS	natural abundance	0.1 mM
14	XPH2	[U-15N]	0.9 mM
15	potassium chloride	natural abundance	150 mM
16	potassium phosphate	natural abundance	50 mM
17	sodium azide	natural abundance	0.01 %

2 3D_13C-separated_NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details 0.6 mM [U-13C; U-15N] XPH2, 50 mM NA- potassium phosphate, 150 mM NA- potassium chloride, 0.01 % NA- sodium azide, 0.1 mM NA- DSS, 1 M [U-2H] trimethylamine oxide, 100% D2O

#	Name	Isotope labeling	Concentration
7	DSS	natural abundance	0.1 mM
8	XPH2	[U-13C; U-15N]	0.6 mM
9	potassium chloride	natural abundance	150 mM
10	potassium phosphate	natural abundance	50 mM
11	sodium azide	natural abundance	0.01 %
12	trimethylamine oxide	[U-2H]	1 M

3 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details 0.8 mM [U-13C; U-15N] XPH2, 50 mM NA- potassium phosphate, 150 mM NA- potassium chloride, 0.01 % NA- sodium azide, 0.1 mM NA- DSS, 1 M [U-2H] trimethylamine oxide, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	DSS	natural abundance	0.1 mM
2	XPH2	[U-13C; U-15N]	0.8 mM
3	potassium chloride	natural abundance	150 mM
4	potassium phosphate	natural abundance	50 mM
5	sodium azide	natural abundance	0.01 %
6	trimethylamine oxide	[U-2H]	1 M

4 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DSS	natural abundance	0.1 mM
2	XPH2	[U-13C; U-15N]	0.8 mM
3	potassium chloride	natural abundance	150 mM
4	potassium phosphate	natural abundance	50 mM
5	sodium azide	natural abundance	0.01 %
6	trimethylamine oxide	[U-2H]	1 M

5 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DSS	natural abundance	0.1 mM
2	XPH2	[U-13C; U-15N]	0.8 mM
3	potassium chloride	natural abundance	150 mM
4	potassium phosphate	natural abundance	50 mM
5	sodium azide	natural abundance	0.01 %
6	trimethylamine oxide	[U-2H]	1 M

6 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DSS	natural abundance	0.1 mM
2	XPH2	[U-13C; U-15N]	0.8 mM
3	potassium chloride	natural abundance	150 mM
4	potassium phosphate	natural abundance	50 mM
5	sodium azide	natural abundance	0.01 %
6	trimethylamine oxide	[U-2H]	1 M

7 2D 1H-13C HSQC aliphatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details 1.6 mM [U-10% 13C] XPH2, 50 mM NA- potassium phosphate, 150 mM NA- potassium chloride, 0.01 % NA- sodium azide, 0.1 mM NA- DSS, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
18	DSS	natural abundance	0.1 mM
19	XPH2	[U-10% 13C]	1.6 mM
20	potassium chloride	natural abundance	150 mM
21	potassium phosphate	natural abundance	50 mM
22	sodium azide	natural abundance	0.01 %

8 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
13	DSS	natural abundance	0.1 mM
14	XPH2	[U-15N]	0.9 mM
15	potassium chloride	natural abundance	150 mM
16	potassium phosphate	natural abundance	50 mM
17	sodium azide	natural abundance	0.01 %

NMR combined restraints 8 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30310_5w8z.nef
Input source #2: Coordindates	5w8z.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
MKKIPLSKYLEEHGTQSALAAALGVNQSAISQMVRAGRCIDIELYTDGRVECRELRPDVFGALEHHHHHH
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MKKIPLSKYLEEHGTQSALAAALGVNQSAISQMVRAGRCIDIELYTDGRVECRELRPDVFGALEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	70	0	0	100.0

Content subtype: combined_30310_5w8z.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	629		88.6 (chain: A, length: 70)
1	Distance restraints	DYANA/DIANA_distance_constraints_4	OK	543 (1)	noe	88.6 (chain: A, length: 70)
2	Distance restraints	CNS/XPLOR_distance_constraints_7	OK	151 (1)	noe	87.1 (chain: A, length: 70)
3	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	28 (1)	hbond	37.1 (chain: A, length: 70)
4	Distance restraints	CNS/XPLOR_distance_constraints_5	OK	28 (1)	hbond	37.1 (chain: A, length: 70)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	120 (120)	.	84.3 (chain: A, length: 70)
2	Dihedral angle restraints	CNS/XPLOR_dihedral_6	OK	120 (120)	.	84.3 (chain: A, length: 70)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 70, Sequence coverage: 88.6%
- Total number of assignments
  - ¹H chemical shifts: 338
  - ¹³C chemical shifts: 227
  - ¹⁵N chemical shifts: 64
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	413	338	81.8
¹³C chemical shifts	311	227	73.0
¹⁵N chemical shifts	77	64	83.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	143	125	87.4
¹³C chemical shifts	140	118	84.3
¹⁵N chemical shifts	68	58	85.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	270	213	78.9
¹³C chemical shifts	171	109	63.7
¹⁵N chemical shifts	9	6	66.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	41	39	95.1
¹³C chemical shifts	41	39	95.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	27	12	44.4
¹³C chemical shifts	27	2	7.4

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_4
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 70, Sequence coverage: 88.6%
- Total number of restraints: 543
- Weight of restraints: 1.0 (543)
- Potential type of restraints: upper-bound-parabolic (543)
- Range of distance target values: 2.5, 7.0 (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_7
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 70, Sequence coverage: 87.1%
  - Total number of restraints: 151
  - Weight of restraints: 1.0 (151)
  - Potential type of restraints: square-well-parabolic (151)
  - Range of distance target values: 1.25, 3.5 (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: DYANA/DIANA_distance_constraints_2
    - Status: OK
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 70, Sequence coverage: 37.1%
    - Total number of restraints: 28
    - Weight of restraints: 1.0 (28)
    - Potential type of restraints: upper-bound-parabolic (28)
    - Range of distance target values: 2.5, 3.5 (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: OK
      - Experiment type: hbond
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 70, Sequence coverage: 37.1%
      - Total number of restraints: 28
        Medium range restraints, 1 < | i - j | < 5 : 28
      - Weight of restraints: 1.0 (28)
        Medium range restraints, 1 < | i - j | < 5 : 1.0 (28)
      - Potential type of restraints: square-well-parabolic (28)
        Medium range restraints, 1 < | i - j | < 5 : square-well-parabolic (28)
      - Range of distance target values: 1.25, 1.75 (Å)
      - Histogram of distance target values
      - Distance restraints per residue
        Chain_ID: A
      - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 70, Sequence coverage: 84.3%
- Total number of restraints: 120
- Total number of restraints per polymer type: 120
- Weight of restraints: 1.0 (120)
- Potential type of restraints: square-well-parabolic (120)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
- Saveframe: CNS/XPLOR_dihedral_6
  - Status: OK
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 70, Sequence coverage: 84.3%
  - Total number of restraints: 120
  - Total number of restraints per polymer type: 120
  - Weight of restraints: 1.0 (120)
  - Potential type of restraints: square-well-parabolic (120)
  - Plot of Phi-Psi angle restraints
  - Dihedral angle restraints per residue
    - Chain_ID: A

Keywords conformational switch, disulfide bond, helix-turn-helix, metamorphic protein, structural evolution, transcription factor

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Found 1 Document (0.329 seconds)

BMRB: 30310

Sample #1

Sample #2

Sample #3

Sample #4

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. XPH2, : 1 : 14 entities Detail

Experiments performed 8 experiments Detail

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NMR combined restraints 8 contents Detail