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BMRB: 25712

2N5F

Solution structure of the dehydroascorbate reductase 3A from Populus trichocarpa

Authors

Roret, T., Tsan, P.

Assembly

dehydroascorbate reductase 3A from Populus trichocarpa

Entity

1. dehydroascorbate reductase 3A from Populus trichocarpa (polymer, Thiol state: free and disulfide bound), 217 monomers, 24188.71 Da Detail

MALEICVKAA VGAPNILGDC PFCQRVLLSL EEKKIPYKSH LINLGDKPQW FLEISPEGKV PVVKIDDKWV ADSDVIVGIL EEKNPEPPLA TPPEFASVGS KIFPSFVKFL KSKDPNDGTE QALLEELKAL DGHLKVHGPF IAGEKITAVD LSLAPKLYHL EVALGHFKNW PIPDNLTHVL NYIKLLFSRE SFKKTRAAEE HVIAGWEPKV NAHHHHH

Formula weight

24188.71 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS20:SG	1:CYS23:SG

Source organism

Populus trichocarpa

Exptl. method

Refine. method

simulated annealing, water refinement

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.2 %, Completeness: 68.3 %, Completeness (bb): 91.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	68.3 % (1774 of 2597)	71.9 % (972 of 1351)	57.6 % (594 of 1032)	97.2 % (208 of 214)
Backbone	91.5 % (1159 of 1266)	95.6 % (409 of 428)	87.0 % (556 of 639)	97.5 % (194 of 199)
Sidechain	51.2 % (786 of 1536)	61.0 % (563 of 923)	34.9 % (209 of 598)	93.3 % (14 of 15)
Aromatic	30.0 % (66 of 220)	54.5 % (60 of 110)	2.8 % (3 of 106)	75.0 % (3 of 4)
Methyl	47.8 % (128 of 268)	71.6 % (96 of 134)	23.9 % (32 of 134)

1. Pt-DHAR3A

MALEICVKAA VGAPNILGDC PFCQRVLLSL EEKKIPYKSH LINLGDKPQW FLEISPEGKV PVVKIDDKWV ADSDVIVGIL EEKNPEPPLA TPPEFASVGS KIFPSFVKFL KSKDPNDGTE QALLEELKAL DGHLKVHGPF IAGEKITAVD LSLAPKLYHL EVALGHFKNW PIPDNLTHVL NYIKLLFSRE SFKKTRAAEE HVIAGWEPKV NAHHHHH

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	Pt-DHAR3A	[U-100% 13C; U-100% 15N]		0.7 ~ 1.3 mM
2	sodium phosphate	natural abundance		50 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2N5F, Strand ID: A Detail

Release date

2016-03-13

Citation

Insights into ascorbate regeneration in plants: investigating the redox and structural properties of dehydroascorbate reductases from Populus trichocarpa
Lallement, P., Roret, T., Tsan, P., M. Gualberto, J., Girardet, J., Didierjean, C., Rouhier, N., Hecker, A.
Biochem. J. (2016), 473, 717-731, PubMed 26699905 , DOI 10.1042/BJ20151147 , Abstract

Related entities 1. dehydroascorbate reductase 3A from Populus trichocarpa, : 1 : 1 : 1 : 156 entities Detail

Experiments performed 9 experiments Detail

1 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

#	Name	Isotope labeling	Type	Concentration
1	Pt-DHAR3A	[U-100% 13C; U-100% 15N]		0.7 ~ 1.3 mM
2	sodium phosphate	natural abundance		50 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

2 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	Pt-DHAR3A	[U-100% 13C; U-100% 15N]		0.7 ~ 1.3 mM
2	sodium phosphate	natural abundance		50 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

3 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	Pt-DHAR3A	[U-100% 13C; U-100% 15N]		0.7 ~ 1.3 mM
2	sodium phosphate	natural abundance		50 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

4 3D HN(CO)CA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	Pt-DHAR3A	[U-100% 13C; U-100% 15N]		0.7 ~ 1.3 mM
2	sodium phosphate	natural abundance		50 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

5 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	Pt-DHAR3A	[U-100% 13C; U-100% 15N]		0.7 ~ 1.3 mM
2	sodium phosphate	natural abundance		50 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

6 3D 1H-15N TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	Pt-DHAR3A	[U-100% 13C; U-100% 15N]		0.7 ~ 1.3 mM
2	sodium phosphate	natural abundance		50 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

7 3D 1H-13C NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	Pt-DHAR3A	[U-100% 13C; U-100% 15N]		0.7 ~ 1.3 mM
2	sodium phosphate	natural abundance		50 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

8 3D HNHA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	Pt-DHAR3A	[U-100% 13C; U-100% 15N]		0.7 ~ 1.3 mM
2	sodium phosphate	natural abundance		50 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

9 3D HCACO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6

#	Name	Isotope labeling	Type	Concentration
1	Pt-DHAR3A	[U-100% 13C; U-100% 15N]		0.7 ~ 1.3 mM
2	sodium phosphate	natural abundance		50 mM
3	H2O	natural abundance		90 %
4	D2O	natural abundance		10 %

NMR combined restraints 2 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts	combined_25712_2n5f.nef
Input source #2: Coordindates	2n5f.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	Error

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-------100
MALEICVKAAVGAPNILGDCPFCQRVLLSLEEKKIPYKSHLINLGDKPQWFLEISPEGKVPVVKIDDKWVADSDVIVGILEEKNPEPPLATPPEFASVGS
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MALEICVKAAVGAPNILGDCPFCQRVLLSLEEKKIPYKSHLINLGDKPQWFLEISPEGKVPVVKIDDKWVADSDVIVGILEEKNPEPPLATPPEFASVGS

-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200
KIFPSFVKFLKSKDPNDGTEQALLEELKALDGHLKVHGPFIAGEKITAVDLSLAPKLYHLEVALGHFKNWPIPDNLTHVLNYIKLLFSRESFKKTRAAEE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
KIFPSFVKFLKSKDPNDGTEQALLEELKALDGHLKVHGPFIAGEKITAVDLSLAPKLYHLEVALGHFKNWPIPDNLTHVLNYIKLLFSRESFKKTRAAEE

-------210--------
HVIAGWEPKVNAHHHHHH
||||||||||||||||||
HVIAGWEPKVNAHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	218	0	0	100.0

Content subtype: combined_25712_2n5f.nef

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1682		97.7 (chain: A, length: 218)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 218, Sequence coverage: 97.7%

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
MALEICVKAAVGAPNILGDCPFCQRVLLSLEEKKIPYKSHLINLGDKPQWFLEISPEGKVPVVKIDDKWVADSDVIVGILEEKNPEPPLATPPEFASVGS
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||  |||||||||||||
MALEICVKAAVGAPNILGDCPFCQRVLLSLEEKKIPYKSHLINLGDKPQWFLEISPEGKVPVVKIDDKWVADSDVIVGILEEKNP..PLATPPEFASVGS
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200
KIFPSFVKFLKSKDPNDGTEQALLEELKALDGHLKVHGPFIAGEKITAVDLSLAPKLYHLEVALGHFKNWPIPDNLTHVLNYIKLLFSRESFKKTRAAEE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
KIFPSFVKFLKSKDPNDGTEQALLEELKALDGHLKVHGPFIAGEKITAVDLSLAPKLYHLEVALGHFKNWPIPDNLTHVLNYIKLLFSRESFKKTRAAEE
-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200

-------210--------
HVIAGWEPKVNAHHHHHH
|||||| |||||||| | 
HVIAGW.PKVNAHHH.H 
-------210-------

Total number of assignments
- ¹H chemical shifts: 933
- ¹³C chemical shifts: 542
- ¹⁵N chemical shifts: 207

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
33	LYS	HZ1	6.748
33	LYS	HZ2	6.748
33	LYS	HZ3	6.748
37	TYR	HH	6.439
135	LYS	HZ1	6.849
135	LYS	HZ2	6.849
135	LYS	HZ3	6.849
137	HIS	HE2	7.054
159	HIS	HD1	3.31
168	LYS	HZ1	7.858
168	LYS	HZ2	7.858
168	LYS	HZ3	7.858
209	LYS	HZ1	7.016
209	LYS	HZ2	7.016
209	LYS	HZ3	7.016
209	LYS	NZ	113.117
213	HIS	HD1	4.698

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	1357	917	67.6
¹³C chemical shifts	1037	542	52.3
¹⁵N chemical shifts	218	206	94.5

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	430	410	95.3
¹³C chemical shifts	436	382	87.6
¹⁵N chemical shifts	200	192	96.0

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	927	507	54.7
¹³C chemical shifts	601	160	26.6
¹⁵N chemical shifts	18	14	77.8

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	135	87	64.4
¹³C chemical shifts	135	15	11.1

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	112	59	52.7
¹³C chemical shifts	108	0	0.0
¹⁵N chemical shifts	4	3	75.0

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

Keywords DHAR, GST, NMR