← Back to search

1c39

STRUCTURE OF CATION-DEPENDENT MANNOSE 6-PHOSPHATE RECEPTOR BOUND TO PENTAMANNOSYL PHOSPHATE

Method: X-RAY DIFFRACTION D_max: 66.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	1c39
deposition_date	1999-07-25
title	STRUCTURE OF CATION-DEPENDENT MANNOSE 6-PHOSPHATE RECEPTOR BOUND TO PENTAMANNOSYL PHOSPHATE
keywords	RECEPTOR, CATION DEPENDENT MANNOSE 6-PHOSPHATE, P-TYPE LECT TRANSPORT, SIGNALING PROTEIN; SIGNALING PROTEIN
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	21.16 Å
rg_electron	19.90 Å
i0	25715000.00
molecular_weight	36478.0 kDa
excluded_volume	44674 Å³
envelope_volume	53437 Å³
shell_volume	22135 Å³
envelope_diameter	68.4 Å
shell_rg	26.54 Å
envelope_rg	20.06 Å
shape_rg	19.87 Å
total_rg	20.81 Å
total_atoms	2540
n_residues	304
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	66.9 Å
rg_real	21.03 Å
rg_real_error	0.34 Å
i0_real	2.5710e+07
i0_real_error	3.2410e+05
rg_reciprocal	21.05 Å
i0_reciprocal	25720000.0000
total_estimate	0.8986
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	27.6 Å
skewness	0.140
kurtosis	-0.413
angular_range	— – 0.3750 Å⁻¹
current_alpha	0.0000
highest_alpha	3600000.0000
n_real_points	69
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.895; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.997

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (5)

Entity 1 polymer

description	CATION-DEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR
formula_weight	17213.4 kDa
mutation	N31Q, N57Q, N68Q, N87Q
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	2711

EKTCDLVGEKGKESEKELALLKRLTPLFQKSFESTVGQSPDMYSYVFRVCREAGQHSSGAGLVQIQKSNGKETVVGRFNETQIFQGSNWIMLIYKGGDEYDNHCGREQRRAVVMISCNRHTLADNFNPVSEERGKVQDCFYLFEMDSSLACS

Source

organism	Bos taurus
common_name	cattle
ncbi_taxonomy_id	9913
host_organism	Trichoplusia ni

Entity 2 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	man
entity_count	2

Entity 3 branched

description	6-O-phosphono-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose
formula_weight	584.4 kDa
src_method	man
entity_count	2

Entity 4 non-polymer

description	MANGANESE (II) ION
formula_weight	54.9 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	171

▶

6. Citations (2)

▶

length_a	42.840 Å
length_b	79.310 Å
length_c	55.570 Å
angle_alpha	90.00 °
angle_beta	100.33 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.850 Å
resolution_low	40.000 Å
r_factor	0.2100
r_work	0.2100
r_free	0.2460

fit	/app/data/saxs_computation/c3/1c39/1c39.fit
pddf	/app/data/pr_computation/c3/1c39/1c39.pr.out
profile	/app/data/saxs_computation/c3/1c39/1c39.dat