BMRB Entry 17546

Name: Refined Structural Basis for the Photoconversion of A Phytochrome to the Activated FAR-RED LIGHT-ABSORBING Form
Published: 2011-05-03

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PDB ID: 2lb5
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR17546
MolProbity Validation Chart

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3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

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

Deposition date:

2011-03-23

Original release date:

2011-05-03

Authors:

Cornilescu, Claudia; Cornilescu, Gabriel; Ulijasz, Andrew; Vierstra, Richard; Markley, John

Citation:

Citation: Ulijasz, Andrew; Cornilescu, Gabriel; Cornilescu, Claudia; Zhang, Junrui; Rivera, Mario; Markley, John; Vierstra, Richard. "Structural basis for the photoconversion of a phytochrome to the activated Pfr form" Nature 463, 250-254 (2010).
PubMed: 20075921

Assembly members:

Assembly members:
Phytochrome, polymer, 164 residues, 18968.801 Da.

Natural source:

Natural source: Common Name: Synechococcus SP Taxonomy ID: 1131 Superkingdom: Bacteria Kingdom: not available Genus/species: Synechococcus SP

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: PGEX-4T

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Phytochrome: PSRLIRQSLDQILRATVEEV RAFLGTDRVKVYRFDPEGHG TVVAEARGGERLPSLLGLTF AGDIEARRLFRLAQVRVIVD VEAQSRSISQWSARVEPLQR PVDPXHVHYLKSMGVASSLV VPLMHHQELWGLLVSHHAEP YSQEQVVLLADQVSIAIAQA ELSL

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	587
15N chemical shifts	148
1H chemical shifts	755

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Phytochrome	1

Entities:

Entity 1, Phytochrome 164 residues - 18968.801 Da.

1

PRO

SER

ARG

LEU

ILE

ARG

GLN

SER

LEU

ASP

2

GLN

ILE

LEU

ARG

ALA

THR

VAL

GLU

VAL

3

ARG

ALA

PHE

LEU

GLY

THR

ASP

ARG

VAL

LYS

4

VAL

TYR

ARG

PHE

ASP

PRO

GLU

GLY

HIS

GLY

5

THR

VAL

ALA

GLU

ALA

ARG

GLY

GLU

6

ARG

LEU

PRO

SER

LEU

GLY

LEU

THR

PHE

7

ALA

GLY

ASP

ILE

GLU

ALA

ARG

LEU

PHE

8

ARG

LEU

ALA

GLN

VAL

ARG

VAL

ILE

VAL

ASP

9

VAL

GLU

ALA

GLN

SER

ARG

SER

ILE

SER

GLN

10

TRP

SER

ALA

ARG

VAL

GLU

PRO

LEU

GLN

ARG

11

PRO

VAL

ASP

PRO

CYC

HIS

VAL

HIS

TYR

LEU

12

LYS

SER

MET

GLY

VAL

ALA

SER

LEU

VAL

13

VAL

PRO

LEU

MET

HIS

GLN

GLU

LEU

TRP

14

GLY

LEU

VAL

SER

HIS

ALA

GLU

PRO

15

TYR

SER

GLN

GLU

GLN

VAL

LEU

ALA

16

ASP

GLN

VAL

SER

ILE

ALA

ILE

ALA

GLN

ALA

17

GLU

LEU

SER

LEU

Samples:

sample_1: Phytochrome, [U-13C; U-15N], 1 – 2 mM; H2O 93%; D2O 7%

sample_conditions_1: ionic strength: 10 mM; pH: 8.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1

Software:

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - geometry optimization, refinement, structure solution

PIPP, Garrett - chemical shift assignment, data analysis, peak picking

NMR spectrometers:

Varian INOVA 800 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks