BMRBj - BMREntryMaster

Found 1 Document (0.7 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

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.7 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

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 2 contents Detail