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BMRB: 30309

5W8Y

Solution Structure of XPH1, 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

protein XPH1

Entity

1. protein XPH1 (polymer, Thiol state: all disulfide bound), 73 monomers, 8022.008 Da Detail

MNAIDIAINK LGSVSALAAA LGVNQSAISQ WRARGRVPAG RCIDIELYTD GRVECRELRP DVFGALEHHH HHH

Formula weight

8022.008 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS42:SG	1:CYS55:SG

Source organism

Xylella fastidiosa subsp. sandyi Ann-1

Exptl. method

solution NMR

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 94.5 %, Completeness: 87.6 %, Completeness (bb): 92.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	87.6 % (708 of 808)	91.6 % (381 of 416)	81.0 % (255 of 315)	93.5 % (72 of 77)
Backbone	92.9 % (403 of 434)	94.0 % (141 of 150)	92.0 % (196 of 213)	93.0 % (66 of 71)
Sidechain	83.0 % (366 of 441)	90.2 % (240 of 266)	71.0 % (120 of 169)	100.0 % (6 of 6)
Aromatic	44.4 % (24 of 54)	44.4 % (12 of 27)	42.3 % (11 of 26)	100.0 % (1 of 1)
Methyl	100.0 % (90 of 90)	100.0 % (45 of 45)	100.0 % (45 of 45)

1. entity 1

MNAIDIAINK LGSVSALAAA LGVNQSAISQ WRARGRVPAG RCIDIELYTD GRVECRELRP DVFGALEHHH HHH

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details 0.4 mM [U-13C; U-15N] XPH1, 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
1	DSS	natural abundance	0.1 mM
2	XPH1	[U-13C; U-15N]	0.4 mM
3	potassium chloride	natural abundance	150 mM
4	potassium phosphate	natural abundance	50 mM
5	sodium azide	natural abundance	0.01 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details 0.4 mM [U-13C; U-15N] XPH1, 50 mM NA- potassium phosphate, 150 mM NA- potassium chloride, 0.01 % NA- sodium azide, 0.1 mM NA- DSS, 100% D2O

#	Name	Isotope labeling	Concentration
6	DSS	natural abundance	0.1 mM
7	XPH1	[U-13C; U-15N]	0.4 mM
8	potassium chloride	natural abundance	150 mM
9	potassium phosphate	natural abundance	50 mM
10	sodium azide	natural abundance	0.01 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details 0.6 mM [U-13C; U-15N] XPH1, 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
11	DSS	natural abundance	0.1 mM
12	XPH1	[U-13C; U-15N]	0.6 mM
13	potassium chloride	natural abundance	150 mM
14	potassium phosphate	natural abundance	50 mM
15	sodium azide	natural abundance	0.01 %

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293 K, pH 6.5, Details 1.8 mM [U-10% 13C] XPH1, 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
16	DSS	natural abundance	0.1 mM
17	XPH1	[U-10% 13C]	1.8 mM
18	potassium chloride	natural abundance	150 mM
19	potassium phosphate	natural abundance	50 mM
20	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: -0.18 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: -0.18 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: 0.05 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: -0.14 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

Entries sharing articles BMRB: 1 entries Detail

BMRB: 30310 released on 2017-08-13
Title Solution Structure of XPH2, a Hybrid Sequence of Xfaso 1 and Pfl 6, Two Cro Proteins With Different Folds

Related entities 1. protein XPH1, : 1 : 1 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 0.6 mM [U-13C; U-15N] XPH1, 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
11	DSS	natural abundance	0.1 mM
12	XPH1	[U-13C; U-15N]	0.6 mM
13	potassium chloride	natural abundance	150 mM
14	potassium phosphate	natural abundance	50 mM
15	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 0.4 mM [U-13C; U-15N] XPH1, 50 mM NA- potassium phosphate, 150 mM NA- potassium chloride, 0.01 % NA- sodium azide, 0.1 mM NA- DSS, 100% D2O

#	Name	Isotope labeling	Concentration
6	DSS	natural abundance	0.1 mM
7	XPH1	[U-13C; U-15N]	0.4 mM
8	potassium chloride	natural abundance	150 mM
9	potassium phosphate	natural abundance	50 mM
10	sodium azide	natural abundance	0.01 %

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 0.4 mM [U-13C; U-15N] XPH1, 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
1	DSS	natural abundance	0.1 mM
2	XPH1	[U-13C; U-15N]	0.4 mM
3	potassium chloride	natural abundance	150 mM
4	potassium phosphate	natural abundance	50 mM
5	sodium azide	natural abundance	0.01 %

4 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DSS	natural abundance	0.1 mM
2	XPH1	[U-13C; U-15N]	0.4 mM
3	potassium chloride	natural abundance	150 mM
4	potassium phosphate	natural abundance	50 mM
5	sodium azide	natural abundance	0.01 %

5 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DSS	natural abundance	0.1 mM
2	XPH1	[U-13C; U-15N]	0.4 mM
3	potassium chloride	natural abundance	150 mM
4	potassium phosphate	natural abundance	50 mM
5	sodium azide	natural abundance	0.01 %

6 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	DSS	natural abundance	0.1 mM
2	XPH1	[U-13C; U-15N]	0.4 mM
3	potassium chloride	natural abundance	150 mM
4	potassium phosphate	natural abundance	50 mM
5	sodium azide	natural abundance	0.01 %

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 1.8 mM [U-10% 13C] XPH1, 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
16	DSS	natural abundance	0.1 mM
17	XPH1	[U-10% 13C]	1.8 mM
18	potassium chloride	natural abundance	150 mM
19	potassium phosphate	natural abundance	50 mM
20	sodium azide	natural abundance	0.01 %

8 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
11	DSS	natural abundance	0.1 mM
12	XPH1	[U-13C; U-15N]	0.6 mM
13	potassium chloride	natural abundance	150 mM
14	potassium phosphate	natural abundance	50 mM
15	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_30309_5w8y.nef
Input source #2: Coordindates	5w8y.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:42:CYS:SG	A:55:CYS:SG	oxidized, CA 60.161, CB 36.523 ppm	oxidized, CA 56.849, CB 39.096 ppm	2.022

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---
MNAIDIAINKLGSVSALAAALGVNQSAISQWRARGRVPAGRCIDIELYTDGRVECRELRPDVFGALEHHHHHH
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MNAIDIAINKLGSVSALAAALGVNQSAISQWRARGRVPAGRCIDIELYTDGRVECRELRPDVFGALEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	73	0	0	100.0

Content subtype: combined_30309_5w8y.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	713		94.5 (chain: A, length: 73)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	289 (1)	noe	87.7 (chain: A, length: 73)
2	Distance restraints	DYANA/DIANA_distance_constraints_7	OK	803 (1)	noe	89.0 (chain: A, length: 73)
3	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	42 (1)	hbond	50.7 (chain: A, length: 73)
4	Distance restraints	DYANA/DIANA_distance_constraints_5	OK	42 (1)	hbond	50.7 (chain: A, length: 73)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	120 (120)	.	82.2 (chain: A, length: 73)
2	Dihedral angle restraints	DYANA/DIANA_dihedral_6	OK	120 (120)	.	82.2 (chain: A, length: 73)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 73, Sequence coverage: 94.5%
- Total number of assignments
  - ¹H chemical shifts: 381
  - ¹³C chemical shifts: 255
  - ¹⁵N chemical shifts: 77
- 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	416	381	91.6
¹³C chemical shifts	315	255	81.0
¹⁵N chemical shifts	84	77	91.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	150	141	94.0
¹³C chemical shifts	146	135	92.5
¹⁵N chemical shifts	71	66	93.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	266	240	90.2
¹³C chemical shifts	169	120	71.0
¹⁵N chemical shifts	13	11	84.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	46	46	100.0
¹³C chemical shifts	46	46	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	27	12	44.4
¹³C chemical shifts	26	11	42.3
¹⁵N chemical shifts	1	1	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_4
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 73, Sequence coverage: 87.7%
- Total number of restraints: 289
- Weight of restraints: 1.0 (289)
- Potential type of restraints: square-well-parabolic (289)
- Range of distance target values: 1.38, 3.0 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_7
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 73, Sequence coverage: 89.0%
  - Total number of restraints: 803
  - Weight of restraints: 1.0 (803)
  - Potential type of restraints: upper-bound-parabolic (803)
  - Range of distance target values: 1.56, 6.0 (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_3
    - Status: OK
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 73, Sequence coverage: 50.7%
    - Total number of restraints: 42
    - Weight of restraints: 1.0 (42)
    - Potential type of restraints: square-well-parabolic (42)
    - 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
    - Saveframe: DYANA/DIANA_distance_constraints_5
      - Status: OK
      - Experiment type: hbond
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 73, Sequence coverage: 50.7%
        --------10--------20--------30--------40--------50--------60--------70--- MNAIDIAINKLGSVSALAAALGVNQSAISQWRARGRVPAGRCIDIELYTDGRVECRELRPDVFGALEHHHHHH |||||||||| |||||||| |||||||||| ||||||||| .NAIDIAINKL..VSALAAAL...QSAISQWRAR......RCIDIELYT --------10--------20--------30--------40---------
      - Total number of restraints: 42
        Total hydrogen bond restraints: 42
        O...H-x: 21
        O...h-N: 21
      - Weight of restraints: 1.0 (42)
        Total hydrogen bond restraints: 1.0 (42)
        O...H-x: 1.0 (21)
        O...h-N: 1.0 (21)
      - Potential type of restraints: upper-bound-parabolic (42)
        Total hydrogen bond restraints: upper-bound-parabolic (42)
        O...H-x: upper-bound-parabolic (21)
        O...h-N: upper-bound-parabolic (21)
      - 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
        Chain_ID_1: A - Chain_ID_2: A

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 73, Sequence coverage: 82.2%
- 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: DYANA/DIANA_dihedral_6
  - Status: OK
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 73, Sequence coverage: 82.2%
  - 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 (0.47 seconds)

BMRB: 30309

Sample #1

Sample #2

Sample #3

Sample #4

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 1 entries Detail

Related entities 1. protein XPH1, : 1 : 1 entities Detail

Experiments performed 8 experiments Detail

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NMR combined restraints 8 contents Detail