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Found 1 Document (0.858 seconds)

BMRB: 17546

2LB5

Refined Structural Basis for the Photoconversion of A Phytochrome to the Activated FAR-RED LIGHT-ABSORBING Form

Authors

Cornilescu, C.C., Cornilescu, G., Ulijasz, A.T., Vierstra, R.D., Markley, J.L.

Assembly

Phytochrome

Entity

1. Phytochrome (polymer, Thiol state: not present), 164 monomers, 18756.30 Da Detail

PSRLIRQSLD QILRATVEEV RAFLGTDRVK VYRFDPEGHG TVVAEARGGE RLPSLLGLTF AGDIEARRLF RLAQVRVIVD VEAQSRSISQ WSARVEPLQR PVDPXHVHYL KSMGVASSLV VPLMHHQELW GLLVSHHAEP YSQEQVVLLA DQVSIAIAQA ELSL

Formula weight

18756.3 Da

Source organism

Synechococcus sp.

Exptl. method

solution NMR

Refine. method

simulated annealing, torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.4 %, Completeness: 73.3 %, Completeness (bb): 90.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	73.3 % (1382 of 1886)	64.2 % (626 of 975)	81.8 % (608 of 743)	88.1 % (148 of 168)
Backbone	90.9 % (874 of 962)	84.1 % (275 of 327)	95.2 % (457 of 480)	91.6 % (142 of 155)
Sidechain	60.9 % (656 of 1078)	54.2 % (351 of 648)	71.7 % (299 of 417)	46.2 % (6 of 13)
Aromatic	45.7 % (53 of 116)	53.4 % (31 of 58)	37.5 % (21 of 56)	50.0 % (1 of 2)
Methyl	76.1 % (175 of 230)	75.7 % (87 of 115)	76.5 % (88 of 115)

1. Phytochrome

PSRLIRQSLD QILRATVEEV RAFLGTDRVK VYRFDPEGHG TVVAEARGGE RLPSLLGLTF AGDIEARRLF RLAQVRVIVD VEAQSRSISQ WSARVEPLQR PVDPXHVHYL KSMGVASSLV VPLMHHQELW GLLVSHHAEP YSQEQVVLLA DQVSIAIAQA ELSL

Show sample condition

Sample

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 8.5 (±0.1)

#	Name	Isotope labeling	Concentration
1	Phytochrome	[U-13C; U-15N]	1.0 ~ 2.0 (±0.1) mM
2	H2O	natural abundance	93 %
3	D2O	natural abundance	7 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.773 ppm	internal	indirect	0.2514495
¹H	water	protons	4.773 ppm	internal	direct	1.0
¹⁵N	water	protons	4.773 ppm	internal	indirect	0.1013291

Referencing offset: -0.15 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.773 ppm	internal	indirect	0.2514495
¹H	water	protons	4.773 ppm	internal	direct	1.0
¹⁵N	water	protons	4.773 ppm	internal	indirect	0.1013291

Referencing offset: -0.15 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.773 ppm	internal	indirect	0.2514495
¹H	water	protons	4.773 ppm	internal	direct	1.0
¹⁵N	water	protons	4.773 ppm	internal	indirect	0.1013291

Referencing offset: -0.11 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.773 ppm	internal	indirect	0.2514495
¹H	water	protons	4.773 ppm	internal	direct	1.0
¹⁵N	water	protons	4.773 ppm	internal	indirect	0.1013291

Referencing offset: -0.07 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2LB5, Strand ID: A Detail

Release date

2011-05-02

Citation

Structural basis for the photoconversion of a phytochrome to the activated Pfr form
Ulijasz, A.T., Cornilescu, G., Cornilescu, C.C., Zhang, J., Rivera, M., Markley, J.L., Vierstra, R.D.
Nature (2010), 463, 250-254, PubMed 20075921 , DOI 10.1038/nature08671 , Abstract

Related entities 1. Phytochrome, : 1 : 99 entities Detail

Experiments performed 2 experiments Detail

NMR combined restraints 8 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_17546_2lb5.nef
Input source #2: Coordindates	2lb5.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	Warning

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)
1:138:CYS:SG	2:1:CYC:CAC	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	CYC	PHYCOCYANOBILIN	Assigned chemical shifts

Sequence alignments

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

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
MDTETWAAAARPSRDALINRITHQIRQSLELDQILRATVEEVRAFLGTDRVKVYRFDPEGHGTVVAEARGGERLPSLLGLTFPAGDIPEEARRLFRLAQV
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MDTETWAAAARPSRDALINRITHQIRQSLELDQILRATVEEVRAFLGTDRVKVYRFDPEGHGTVVAEARGGERLPSLLGLTFPAGDIPEEARRLFRLAQV

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

--------
SLHHHHHH
||||||||
SLHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	208	0	0	100.0

Content subtype: combined_17546_2lb5.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1296		75.5 (chain: A, length: 208), 100.0 (chain: B, length: 1)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	1277 (1)	noe	67.3 (chain: A, length: 208)
2	Distance restraints	CNS/XPLOR_distance_constraints_8	Warning	778 (1)	noe	61.1 (chain: A, length: 208)
3	Distance restraints	CNS/XPLOR_distance_constraints_7	OK	156 (1)	hbond	49.5 (chain: A, length: 208)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	477 (477)	.	81.7 (chain: A, length: 208)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_5	Warning	249 (243)	.	70.7 (chain: A, length: 208)
2	RDC restraints	CNS/XPLOR_dipolar_coupling_6	Warning	39 (39)	.	18.8 (chain: A, length: 208)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 208, Sequence coverage: 75.5%
  - Entity_assembly_ID: B, Chain length: 1, Sequence coverage: 100.0%
- Total number of assignments
  - ¹³C chemical shifts: 571
  - ¹H chemical shifts: 582
  - ¹⁵N chemical shifts: 143
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- 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)
169	HIS	HE2	10.07

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	941	568	60.4
¹H chemical shifts	1239	577	46.6
¹⁵N chemical shifts	230	142	61.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	416	291	70.0
¹H chemical shifts	414	266	64.3
¹⁵N chemical shifts	195	136	69.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	525	277	52.8
¹H chemical shifts	825	311	37.7
¹⁵N chemical shifts	35	6	17.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	138	80	58.0
¹H chemical shifts	138	80	58.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	75	21	28.0
¹H chemical shifts	78	31	39.7
¹⁵N chemical shifts	3	1	33.3

Comp_index_ID	Comp_ID
1	CYC

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 208, Sequence coverage: 67.3%
- Total number of restraints: 1218
- Weight of restraints: 1.0 (1218)
- Potential type of restraints: square-well-parabolic (1218)
- Range of distance target values: 1.25, 4.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_8
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 208, Sequence coverage: 61.1%
  - Total number of restraints: 753
  - Weight of restraints: 1.0 (753)
  - Potential type of restraints: square-well-parabolic (753)
  - Range of distance target values: 1.1, 4.8 (Å)
  - Histogram of distance target values
  - Histogram of discrepancy in distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_7
    - Status: OK
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 208, Sequence coverage: 49.5%
    - Total number of restraints: 156
    - Weight of restraints: 1.0 (156)
    - Potential type of restraints: square-well-parabolic (156)
    - Range of distance target values: 2.0, 3.0 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
        None
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 208, Sequence coverage: 81.7%
- Total number of restraints: 477
- Total number of restraints per polymer type: 477
- Weight of restraints: 1.0 (477)
- Potential type of restraints: square-well-parabolic (477)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_5
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 208, Sequence coverage: 70.7%
- Total number of restraints: 249
- Potential type of restraints: square-well-parabolic (249)
- Range of observed RDC values: -21.4, 19.5 (Hz)
- Histogram of observed RDC values
- RDC restraints per residue
  - Chain_ID: A
    None
- Saveframe: CNS/XPLOR_dipolar_coupling_6
  - Status: Warning
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 208, Sequence coverage: 18.8%
  - Total number of restraints: 39
  - Potential type of restraints: square-well-parabolic (39)
  - Range of observed RDC values: -24.6, 23.1 (Hz)
  - Histogram of observed RDC values
  - RDC restraints per residue

Keywords GAF domain, KINASE, PHOSPHOPROTEIN, PHYTOCHROME, TRANSFERASE

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Found 1 Document (0.858 seconds)

BMRB: 17546

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Phytochrome, : 1 : 99 entities Detail

Experiments performed 2 experiments Detail

Instrument

Sample

Instrument

Sample

NMR combined restraints 8 contents Detail