BMRBj - BMREntryMaster

Found 1 Document (0.719 seconds)

BMRB: 19213

2M7U

Blue Light-Absorbing State of TePixJ, an Active Cyanobacteriochrome Domain

Authors

Cornilescu, G., Cornilescu, C.C., Burgie, S.E., Walker, J.M., Markley, J.L., Ulijasz, A.T., Vierstra, R.D.

Assembly

TePixJ

Entity

1. TePixJ (polymer, Thiol state: free and other bound), 165 monomers, 18750.13 Da Detail

MAAVQLSELR DRQAIFETLV AKGRELLACD RVIVYAFDDN YVGTVVAESV AEGWPQARDQ VIEDPCFREH WVEAYRQGRI QATTDIFKAG LTECHLNQLR PLKVRANLVV PMVIDDQLFG LLIAHQASEP RQWQEIEIDQ FSELASTGSL VLERLHFLEQ TIASL

2. PHYCOVIOLOBILIN (non-polymer, Thiol state: not present), 588.694 Da

Total weight

19338.824 Da

Max. entity weight

18750.13 Da

Entity Connection

na 2 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:CYS66:SG	2:PVN1:C16
2	na	sing	1:CYS94:SG	2:PVN1:C02

Source organism

Thermosynechococcus elongatus

Exptl. method

solution NMR

Refine. method

simulated annealing, torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.8 %, Completeness: 85.3 %, Completeness (bb): 93.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	85.3 % (1649 of 1934)	81.9 % (817 of 998)	88.0 % (666 of 757)	92.7 % (166 of 179)
Backbone	93.8 % (919 of 980)	91.0 % (302 of 332)	95.7 % (467 of 488)	93.8 % (150 of 160)
Sidechain	79.7 % (886 of 1112)	77.3 % (515 of 666)	83.1 % (355 of 427)	84.2 % (16 of 19)
Aromatic	56.2 % (82 of 146)	60.3 % (44 of 73)	50.0 % (35 of 70)	100.0 % (3 of 3)
Methyl	82.6 % (185 of 224)	83.0 % (93 of 112)	82.1 % (92 of 112)

1. TePixJ

MAAVQLSELR DRQAIFETLV AKGRELLACD RVIVYAFDDN YVGTVVAESV AEGWPQARDQ VIEDPCFREH WVEAYRQGRI QATTDIFKAG LTECHLNQLR PLKVRANLVV PMVIDDQLFG LLIAHQASEP RQWQEIEIDQ FSELASTGSL VLERLHFLEQ TIASL

Show sample condition

Sample

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 8, Details 13C/15N labeled TePixJ with unlabeled PVN, unlabeled TePixJ with 13C/15N labeled PVN in Pb

#	Name	Isotope labeling	Concentration
1	TePixJ	[U-13C; U-15N]	0.7 ~ 1.3 (±0.1) mM
2	PHYCOVIOLOBILIN	natural abundance	0.7 ~ 1.3 (±0.2) mM
3	H2O	natural abundance	93 %
4	D2O	natural abundance	7 %

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: 0.0 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: 0.0 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: 0.24 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2M7U, Strand ID: A Detail

Release date

2014-01-01

Citation

Dynamic structural changes underpin photoconversion of a blue/green cyanobacteriochrome between its dark and photoactivated states
Cornilescu, C.C., Cornilescu, G., Burgie, E., Markley, J.L., Ulijasz, A.T., Vierstra, R.D.
J. Biol. Chem. (2014), 289, 3055-3065, PubMed 24337572 , DOI 10.1074/jbc.M113.531053 , Abstract

Related entities 1. TePixJ, : 1 : 3 : 5 : 35 entities Detail

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 8, Details 13C/15N labeled TePixJ with unlabeled PVN, unlabeled TePixJ with 13C/15N labeled PVN in Pb

#	Name	Isotope labeling	Concentration
1	TePixJ	[U-13C; U-15N]	0.7 ~ 1.3 (±0.1) mM
2	PHYCOVIOLOBILIN	natural abundance	0.7 ~ 1.3 (±0.2) mM
3	H2O	natural abundance	93 %
4	D2O	natural abundance	7 %

2 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	TePixJ	[U-13C; U-15N]	0.7 ~ 1.3 (±0.1) mM
2	PHYCOVIOLOBILIN	natural abundance	0.7 ~ 1.3 (±0.2) mM
3	H2O	natural abundance	93 %
4	D2O	natural abundance	7 %

3 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	TePixJ	[U-13C; U-15N]	0.7 ~ 1.3 (±0.1) mM
2	PHYCOVIOLOBILIN	natural abundance	0.7 ~ 1.3 (±0.2) mM
3	H2O	natural abundance	93 %
4	D2O	natural abundance	7 %

4 3D HCCH-TOCSY

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	TePixJ	[U-13C; U-15N]	0.7 ~ 1.3 (±0.1) mM
2	PHYCOVIOLOBILIN	natural abundance	0.7 ~ 1.3 (±0.2) mM
3	H2O	natural abundance	93 %
4	D2O	natural abundance	7 %

5 3D 1H-15N NOESY

Instrument

Varian INOVA - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	TePixJ	[U-13C; U-15N]	0.7 ~ 1.3 (±0.1) mM
2	PHYCOVIOLOBILIN	natural abundance	0.7 ~ 1.3 (±0.2) mM
3	H2O	natural abundance	93 %
4	D2O	natural abundance	7 %

6 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	TePixJ	[U-13C; U-15N]	0.7 ~ 1.3 (±0.1) mM
2	PHYCOVIOLOBILIN	natural abundance	0.7 ~ 1.3 (±0.2) mM
3	H2O	natural abundance	93 %
4	D2O	natural abundance	7 %

7 3D 1H-13C NOESY aromatic

Instrument

Varian INOVA - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	TePixJ	[U-13C; U-15N]	0.7 ~ 1.3 (±0.1) mM
2	PHYCOVIOLOBILIN	natural abundance	0.7 ~ 1.3 (±0.2) mM
3	H2O	natural abundance	93 %
4	D2O	natural abundance	7 %

8 3D HNCO

Instrument

Bruker Avance - 700 MHz

Sample

State anisotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 8, Details 13C/15N labeled TePixJ with unlabeled PVN, unlabeled TePixJ with 13C/15N labeled PVN in Pb

#	Name	Isotope labeling	Concentration
1	TePixJ	[U-13C; U-15N]	0.7 ~ 1.3 (±0.1) mM
2	PHYCOVIOLOBILIN	natural abundance	0.7 ~ 1.3 (±0.2) mM
3	H2O	natural abundance	93 %
4	D2O	natural abundance	7 %

NMR combined restraints 2 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts	combined_19213_2m7u.nef
Input source #2: Coordindates	2m7u.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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:94:CYS:SG	2:1:VRB:C02	unknown	unknown	n/a
1:66:CYS:SG	2:1:VRB:C16	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	VRB	Phycoviolobilin, blue light-absorbing form	None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

-430-----440-------450-------460-------470-------480-------490-------500-------510-------520-------5
MAAVQLSELRDRQAIFETLVAKGRELLACDRVIVYAFDDNYVGTVVAESVAEGWPQARDQVIEDPCFREHWVEAYRQGRIQATTDIFKAGLTECHLNQLR
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MAAVQLSELRDRQAIFETLVAKGRELLACDRVIVYAFDDNYVGTVVAESVAEGWPQARDQVIEDPCFREHWVEAYRQGRIQATTDIFKAGLTECHLNQLR
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

30-------540-------550-------560-------570-------580-------590---
PLKVRANLVVPMVIDDQLFGLLIAHQASEPRQWQEIEIDQFSELASTGSLVLERLHFLEQTIASL
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PLKVRANLVVPMVIDDQLFGLLIAHQASEPRQWQEIEIDQFSELASTGSLVLERLHFLEQTIASL
-------110-------120-------130-------140-------150-------160-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	165	0	0	100.0

Content subtype: combined_19213_2m7u.nef

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	2		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1619		96.4 (chain: A, length: 165)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 165, Sequence coverage: 96.4%

-430-----440-------450-------460-------470-------480-------490-------500-------510-------520-------5
MAAVQLSELRDRQAIFETLVAKGRELLACDRVIVYAFDDNYVGTVVAESVAEGWPQARDQVIEDPCFREHWVEAYRQGRIQATTDIFKAGLTECHLNQLR
||||| |||  |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MAAVQ.SEL..RQAIFETLVAKGRELLACDRVIVYAFDDNYVGTVVAESVAEGWPQARDQVIEDPCFREHWVEAYRQGRIQATTDIFKAGLTECHLNQLR

30-------540-------550-------560-------570-------580-------590---
PLKVRANLVVPMVIDDQLFGLLIAHQASEPRQWQEIEIDQFSELASTGSLVLERLHFLEQTIASL
|||||||||||||||||||||||||||||||||||||||||||||||||||  || |||||||||
PLKVRANLVVPMVIDDQLFGLLIAHQASEPRQWQEIEIDQFSELASTGSLV..RL.FLEQTIASL

Total number of assignments
- ¹H chemical shifts: 803
- ¹³C chemical shifts: 645
- ¹⁵N chemical shifts: 171

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
459	ARG	HH11	8.88
459	ARG	HH12	7.0
459	ARG	HH21	9.54
459	ARG	HH22	5.64
459	ARG	NH1	73.2
459	ARG	NH2	74.1
553	HIS	HE2	12.36
553	HIS	NE2	165.8
559	ARG	HH11	7.06
559	ARG	HH21	6.07
559	ARG	NH1	71.0
559	ARG	NH2	69.3

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	998	796	79.8
¹³C chemical shifts	757	645	85.2
¹⁵N chemical shifts	191	166	86.9

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	332	297	89.5
¹³C chemical shifts	330	301	91.2
¹⁵N chemical shifts	160	144	90.0

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	666	499	74.9
¹³C chemical shifts	427	344	80.6
¹⁵N chemical shifts	31	22	71.0

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	114	93	81.6
¹³C chemical shifts	114	91	79.8

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	73	42	57.5
¹³C chemical shifts	70	35	50.0
¹⁵N chemical shifts	3	3	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: A

Covalent bonds

Saveframe: assembly
- Status: OK

Keywords blue/green light-absorbing, cyanobacteria, phycoviolobilin, phytochrome, PixJ, PVB

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Found 1 Document (0.719 seconds)

BMRB: 19213

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. TePixJ, : 1 : 3 : 5 : 35 entities Detail

Experiments performed 8 experiments Detail

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NMR combined restraints 2 contents Detail