BMRBj - BMREntryMaster

Found 1 Document (1.436 seconds)

BMRB: 4154

4JWS

13C and Stereospecific 13C and 1H Resonance Assignments for Oxidized Putidaredoxin

Authors

Jain, N., Lyons, T., Pochapsky, T.C., Kuti, M.

Assembly

oxidized putidaredoxin

Entity

1. putidaredoxin (polymer), 106 monomers, 11418.83 Da Detail

SKVVYVSHDG TRRELDVADG VSLMQAAVSN GIYDIVGDCG GSASCATCHV YVNEAFTDKV PAANEREIGM LECVTAELKP NSRLCCQIIM TPELDGIVVD VPDRQW

2. FES (non-polymer), 175.820 Da

Total weight

11594.65 Da

Max. entity weight

11418.83 Da

Source organism

Pseudomonas putida

Exptl. method

NMR

Refine. method

DG,SA

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 87.7 %, Completeness: 84.7 %, Completeness (bb): 82.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	84.7 % (966 of 1140)	85.6 % (498 of 582)	83.7 % (375 of 448)	84.5 % (93 of 110)
Backbone	82.2 % (516 of 628)	81.0 % (175 of 216)	82.3 % (255 of 310)	84.3 % (86 of 102)
Sidechain	87.4 % (533 of 610)	88.3 % (323 of 366)	86.0 % (203 of 236)	87.5 % (7 of 8)
Aromatic	100.0 % (54 of 54)	100.0 % (27 of 27)	100.0 % (26 of 26)	100.0 % (1 of 1)
Methyl	87.9 % (116 of 132)	89.4 % (59 of 66)	86.4 % (57 of 66)

1. putidaredoxin

SKVVYVSHDG TRRELDVADG VSLMQAAVSN GIYDIVGDCG GSASCATCHV YVNEAFTDKV PAANEREIGM LECVTAELKP NSRLCCQIIM TPELDGIVVD VPDRQW

Show sample condition

Sample

Temperature 290 (±0.2) K, pH 7.4 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	putidaredoxin	[U-13C, U-15N]		1 mM
2	deutero-trisbuffer

LACS Plot; CA

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

Referencing offset: 0.29 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: 0.29 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: 0.21 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: 0.59 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 14 models in PDB: 1PDX, Strand ID: A Detail

Release date

1999-09-27

Citation 1

A refined model for the solution structure of oxidized putidaredoxin
Pochapsky, T.C., Jain, N.U., Lyons, T., Kuti, M.
Biochemistry (1999), 38, 4681-4690, PubMed 10200155 , DOI 10.1021/bi983030b , Abstract

Show more 3 citaions

Citation 2

1H NMR sequential assignments and identification of secondary structural elements in oxidized putidaredoxin, an electron-transfer protein from Pseudomonas
Ye, X.M., Pochapsky, T.C., Pochapsky, S.S.
Biochemistry (1992), 31, 1961-1968, PubMed 1536837 , DOI: , Abstract

Citation 3

Redox-dependent dynamics of putidaredoxin characterized by amide proton exchange
Lyons, T.A., Ratnaswamy, G., Pochapsky, T.C.
Protein Sci. (1996), 5, 627-639, PubMed 8845752 , DOI 10.1002/pro.5560050407 , Abstract

Citation 4

1H, 13C and 15N chemical shift referencing in biomolecular NMR
Wishart, D.S., Bigam, C.G., Yao, J., Abildgaard, F., Dyson, H.J., Oldfield, E., Markley, J.L., Sykes, B.D.
J. Biomol. NMR (1995), 6, 135-140, PubMed 8589602 , DOI: , Abstract

Hide non-primary 3 citaions

Related entities 1. putidaredoxin, : 1 : 5 : 1 : 14 : 113 entities Detail

Interaction partners 1. putidaredoxin, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 4 experiments Detail

Chemical shift validation 4 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr4154_3.str
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

Content subtype: bmr4154_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_one	Warning	1097		84.9 (chain: 1, length: 106)
1	Chemical shift references	chemical_shift_reference_one	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_one

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: 1, Chain length: 106, Sequence coverage: 84.9%

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
SKVVYVSHDGTRRELDVADGVSLMQAAVSNGIYDIVGDCGGSASCATCHVYVNEAFTDKVPAANEREIGMLECVTAELKPNSRLCCQIIMTPELDGIVVD
|||||||||||||||||||||||||||||||||||             |||||||||||||||||||||||||||||||||||   ||||||||||||||
SKVVYVSHDGTRRELDVADGVSLMQAAVSNGIYDI.............HVYVNEAFTDKVPAANEREIGMLECVTAELKPNSR...QIIMTPELDGIVVD

------
VPDRQW
||||||
VPDRQW

Total number of assignments
- ¹H chemical shifts: 625
- ¹³C chemical shifts: 376
- ¹⁵N chemical shifts: 96

Completeness of assignments

Entity_assemble_ID: 1

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
5	TYR	HH	8.02
8	HIS	HD1	9.45
8	HIS	ND1	126.0
8	HIS	NE2	187.0
13	ARG	HH11	6.23
13	ARG	HH12	6.23
13	ARG	HH21	7.2
13	ARG	HH22	7.2
25	GLN	CD	175.5
30	ASN	CG	178.2
49	HIS	HD1	12.01
49	HIS	ND1	167.8
49	HIS	NE2	246.8
53	ASN	CG	176.4
58	ASP	CG	178.9
64	ASN	CG	175.8
81	ASN	CG	178.6
82	SER	HG	10.1
83	ARG	HH11	8.37
83	ARG	HH12	8.37
83	ARG	HH21	5.5
83	ARG	HH22	5.5
105	GLN	CD	179.6

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	582	495	85.1
¹³C chemical shifts	448	369	82.4
¹⁵N chemical shifts	115	92	80.0

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	216	173	80.1
¹³C chemical shifts	212	168	79.2
¹⁵N chemical shifts	102	81	79.4

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	366	322	88.0
¹³C chemical shifts	236	201	85.2
¹⁵N chemical shifts	13	11	84.6

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	69	59	85.5
¹³C chemical shifts	69	59	85.5

Aromatic group atoms

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

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: 1

Keywords adrenodoxin, cytochrome P450, ferredoxin

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Found 1 Document (1.436 seconds)

BMRB: 4154

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. putidaredoxin, : 1 : 5 : 1 : 14 : 113 entities Detail

Interaction partners 1. putidaredoxin, : 1 interactors Detail

Experiments performed 4 experiments Detail

Sample

Sample

Sample

Sample

Chemical shift validation 4 contents Detail