BMRBj - BMREntryMaster

Found 1 Document (0.739 seconds)

BMRB: 19214

2M7V

Green 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

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

Entity

1. Green Light-Absorbing State of TePixJ, an Active Cyanobacteriochrome Domain, entity 1 (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. PHYCOCYANOBILIN (non-polymer), 588.694 Da

Total weight

19338.824 Da

Max. entity weight

18750.13 Da

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: 90.9 %, Completeness: 72.4 %, Completeness (bb): 83.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	72.4 % (1401 of 1934)	69.2 % (691 of 998)	74.6 % (565 of 757)	81.0 % (145 of 179)
Backbone	83.1 % (814 of 980)	81.9 % (272 of 332)	84.0 % (410 of 488)	82.5 % (132 of 160)
Sidechain	65.1 % (724 of 1112)	62.9 % (419 of 666)	68.4 % (292 of 427)	68.4 % (13 of 19)
Aromatic	44.5 % (65 of 146)	49.3 % (36 of 73)	40.0 % (28 of 70)	33.3 % (1 of 3)
Methyl	75.9 % (170 of 224)	77.7 % (87 of 112)	74.1 % (83 of 112)

1. entity 1

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 Pg

#	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: 0.1 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: 0.1 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: -0.02 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: 0.22 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2M7V, 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. Green Light-Absorbing State of TePixJ, an Active Cyanobacteriochrome Domain, entity 1, : 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 Pg

#	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 Pg

#	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_19214_2m7v.nef
Input source #2: Coordindates	2m7v.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:PVN:C31	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	PVN	PHYCOVIOLOBILIN	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_19214_2m7v.nef

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1368		89.1 (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: 89.1%
- Total number of assignments
  - ¹H chemical shifts: 676
  - ¹³C chemical shifts: 547
  - ¹⁵N chemical shifts: 145
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
553	HIS	HE2	11.15
559	ARG	HH21	7.11
559	ARG	HH22	6.04
559	ARG	NH2	70.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	998	673	67.4
¹³C chemical shifts	757	547	72.3
¹⁵N chemical shifts	191	144	75.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	332	267	80.4
¹³C chemical shifts	330	266	80.6
¹⁵N chemical shifts	160	128	80.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	666	406	61.0
¹³C chemical shifts	427	281	65.8
¹⁵N chemical shifts	31	16	51.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	114	88	77.2
¹³C chemical shifts	114	81	71.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	73	36	49.3
¹³C chemical shifts	70	28	40.0
¹⁵N chemical shifts	3	1	33.3

Covalent bonds

Saveframe: assembly
- Status: OK

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

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Found 1 Document (0.739 seconds)

BMRB: 19214

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Green Light-Absorbing State of TePixJ, an Active Cyanobacteriochrome Domain, entity 1, : 1 : 3 : 5 : 35 entities Detail

Experiments performed 8 experiments Detail

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NMR combined restraints 2 contents Detail