← Back to search

9qkp

Structure of the cyanobacteria specific PRK from Chroococcidiopsis (Hyella disjuncta) PCC 6712 (P41212 crystal form)

Method: X-RAY DIFFRACTION D_max: 135.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9qkp
deposition_date	2025-03-20
last_revision	2026-04-08
title	Structure of the cyanobacteria specific PRK from Chroococcidiopsis (Hyella disjuncta) PCC 6712 (P41212 crystal form)
keywords	carbon fixation, sugar kinase, PHOTOSYNTHESIS; PHOTOSYNTHESIS
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	39.75 Å
rg_electron	39.46 Å
i0	306660000.00
molecular_weight	138140.0 kDa
excluded_volume	171080 Å³
envelope_volume	230280 Å³
shell_volume	50022 Å³
envelope_diameter	136.5 Å
shell_rg	43.73 Å
envelope_rg	38.87 Å
shape_rg	39.47 Å
total_rg	39.67 Å
total_atoms	9698
n_residues	1220
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

▼

3. P(r) Analysis (GNOM)

dmax	135.1 Å
rg_real	39.81 Å
rg_real_error	1.13 Å
i0_real	3.0670e+08
i0_real_error	5.5640e+06
rg_reciprocal	39.78 Å
i0_reciprocal	306600000.0000
total_estimate	0.8751
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	54.0 Å
skewness	0.320
kurtosis	-0.385
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	50860000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.854; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.951; Smooth: 0.861

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (6)

Entity 1 polymer

description	cyanobacteria specific phosphoribulokinase from Chroococcidiopsis PCC 6712
formula_weight	35208.0 kDa
ec_number	2.7.1.19
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	9713

MSERPIILGIVGDSAAGKTTLTRGLAQVFGEENVTAICTDDYHRYDRQQRAEMGISALHPDCNYVDIIEQHLDLLRQGKPILKPIYNHNTGKFDPPEYIQPRKYVVVEGLLGYSTRPMRDSYDVKVYLAPPESLRYSWKIKRDTRKRGYTEEQVLEQLKMREHDSENYIRPQRQWADVVVSFYPPDAESEANNLLLNVKLILRPTIPHPNLTNILSAEGNHLGSAIRLGLERDMGKPVDVLSIDGHATAEQVRELEKIFCSEVPFLGQFCSLEGNTEIGTVIGTTGESLQSYPLALTQLLIAYHMLKELGS

Source

organism	[Chroococcidiopsis] sp. PCC 6712
ncbi_taxonomy_id	118675
host_organism	Escherichia coli KRX

Entity 2 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	ADENOSINE-5'-DIPHOSPHATE
formula_weight	427.2 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	RIBULOSE-1,5-DIPHOSPHATE
formula_weight	310.1 kDa
src_method	nat
entity_count	4

Entity 5 non-polymer

description	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
formula_weight	354.4 kDa
src_method	nat
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	15

▶

6. Citations (1)

▶

length_a	92.752 Å
length_b	92.752 Å
length_c	407.667 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	32

space_group	P 41 21 2
int_tables_number	92
crystal_system	tetragonal

resolution	2.430 Å
resolution_low	65.590 Å
r_factor	0.2335
r_work	0.2325
r_free	0.2682

fit	/app/data/saxs_computation/qk/9qkp/9qkp.fit
pddf	/app/data/pr_computation/qk/9qkp/9qkp.pr.out
profile	/app/data/saxs_computation/qk/9qkp/9qkp.dat