SAXSdb — 9rn8

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1. Structure Basics

entry_id	9rn8
deposition_date	2025-06-19
title	;Crystal structure of the photosensory core module (PCM) of a cyano-phenylalanine mutant oCNF205 of the bathy phytochrome Agp2 from Agrobacterium fabrum in the Pfr state. ;
keywords	fluorescent protein, phytochrome, bacteriophytochrome, Pfr-state, ortho-cyano-phenylalanine, Stark labels, SIGNALING PROTEIN; SIGNALING PROTEIN
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	35.49 Å
rg_electron	34.60 Å
i0	185686000.00
molecular_weight	109340.0 kDa
excluded_volume	136780 Å³
envelope_volume	178420 Å³
shell_volume	42756 Å³
envelope_diameter	106.4 Å
shell_rg	41.54 Å
envelope_rg	33.76 Å
shape_rg	34.61 Å
total_rg	35.07 Å
total_atoms	7696
n_residues	957
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	104.6 Å
rg_real	35.31 Å
rg_real_error	0.74 Å
i0_real	1.8570e+08
i0_real_error	3.0360e+06
rg_reciprocal	35.43 Å
i0_reciprocal	185700000.0000
total_estimate	0.9077
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	48.8 Å
skewness	0.014
kurtosis	-0.801
angular_range	— – 0.2250 Å⁻¹
current_alpha	0.0000
highest_alpha	31450000.0000
n_real_points	46
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.980; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.856

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	histidine kinase
formula_weight	56577.3 kDa
ec_number	2.7.13.3
mutation	Y205oCNF
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	8818

MASTDYHVDLTNCDREPIHIPGYIQPHGCLIACDNAMRMVLRHSENCGELLGLEGDLNGRTAEDVLGKKLVHDLRNALTVTGRTTRPAMLPAMETSDGRSFDISLHRYKSTTIIEFEPSGSDAQPLGTARKMVDRIREADSVESLISRTTRLVKATLGYDRVMIYRFQEDGAGKVVSEAKQPELESFLGQYFPASDIPQQARALXLKNTLRIISDASGTRIPVLPAVDVSGEPLDLSYAHLRSVSPIHCEYLRNMGVAASMSISVIVDGALWGLIACHHYSPRVLSMPVRIAAEMFGEFFSMHLQVLKQKRRLDTINHAHAALDRFLRLAAHHANIEELLVDSFQDFADLMPCDGVGLWVGNNWHGHGATPPHDAIPRLARFVASASEGRVWATHALSQAIPEAEIYAGTAAGMLAIPLSQVKSDYLLFFRKEIVQNLNWAGNPEKSYETGPMGDRLTPRKSFAIWKETVRLQAQPWSEADREIAEAARIALVEVAFHHSEHHHHHH

Source

organism	Agrobacterium fabrum str. C58
ncbi_taxonomy_id	176299
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	histidine kinase
formula_weight	56603.4 kDa
ec_number	2.7.13.3
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MASTDYHVDLTNCDREPIHIPGYIQPHGCLIACDNAMRMVLRHSENCGELLGLEGDLNGRTAEDVLGKKLVHDLRNALTVTGRTTRPAMLPAMETSDGRSFDISLHRYKSTTIIEFEPSGSDAQPLGTARKMVDRIREADSVESLISRTTRLVKATLGYDRVMIYRFQEDGAGKVVSEAKQPELESFLGQYFPASDIPQQARALXLKNTLRIISDASGTRIPVLPAVDVSGEPLDLSYAHLRSVSPIHCEYLRNMGVAASMSISVIVDGALWGLIACHHYSPRVLSMPVRIAAEMFGEFFSMHLQVLKQKRRLDTINHAHAALDRFLRLAAHHANIEELLVDSFQDFADLMPCDGVGLWVGNNWHGHGATPPHDAIPRLARFVASASEGRVWATHALSQAIPEAEIYAGTAAGMLAIPLSQVKSDYLLFFRKEIVQNLNWAGNPEKSYETGPMGDRLTPRKSFAIWKETVRLQAQPWSEADREIAEAARIALVEVAFHHSEHHHHHH

Source

organism	Agrobacterium fabrum str. C58
ncbi_taxonomy_id	176299
host_organism	Escherichia coli BL21(DE3)

Entity 3 non-polymer

description	;3-[(2Z)-2-({3-(2-carboxyethyl)-5-[(E)-(4-ethenyl-3-methyl-5-oxo-1,5-dihydro-2H-pyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-2-yl}methylidene)-5-{(Z)-[(3E,4S)-3-ethylidene-4-methyl-5-oxopyrrolidin-2-ylidene]methyl}-4-methyl-2H-pyrrol-3-yl]propanoic acid ;
formula_weight	584.7 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	(4S)-2-METHYL-2,4-PENTANEDIOL
formula_weight	118.2 kDa
src_method	syn
entity_count	4

Entity 5 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
formula_weight	195.2 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	2

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	975

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6. Citations (1)

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length_a	74.411 Å
length_b	93.542 Å
length_c	173.757 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	1.790 Å
resolution_low	41.220 Å
r_factor	0.1791
r_work	0.1777
r_free	0.2069

fit	/app/data/saxs_computation/rn/9rn8/9rn8.fit
pddf	/app/data/pr_computation/rn/9rn8/9rn8.pr.out
profile	/app/data/saxs_computation/rn/9rn8/9rn8.dat

;Crystal structure of the photosensory core module (PCM) of a cyano-phenylalanine mutant oCNF205 of the bathy phytochrome Agp2 from Agrobacterium fabrum in the Pfr state. ;

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction

5. Entities & Polymer Info (8)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)