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1d5c

CRYSTAL STRUCTURE OF PLASMODIUM FALCIPARUM RAB6 COMPLEXED WITH GDP

Method: X-RAY DIFFRACTION D_max: 50.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1d5c
deposition_date	1999-10-06
title	CRYSTAL STRUCTURE OF PLASMODIUM FALCIPARUM RAB6 COMPLEXED WITH GDP
keywords	G-PROTEIN, GTPASE, RAB, RAB6, VESICULAR TRAFFICKING, ENDOCYTOSIS-EXOCYTOSIS COMPLEX; ENDOCYTOSIS/EXOCYTOSIS
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	16.38 Å
rg_electron	15.03 Å
i0	7125570.00
molecular_weight	19186.0 kDa
excluded_volume	23875 Å³
envelope_volume	26862 Å³
shell_volume	14808 Å³
envelope_diameter	50.4 Å
shell_rg	21.19 Å
envelope_rg	15.39 Å
shape_rg	15.03 Å
total_rg	16.14 Å
total_atoms	1340
n_residues	159
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	50.8 Å
rg_real	16.24 Å
rg_real_error	0.22 Å
i0_real	7.1260e+06
i0_real_error	8.2760e+04
rg_reciprocal	16.25 Å
i0_reciprocal	7126000.0000
total_estimate	0.8966
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	21.5 Å
skewness	0.073
kurtosis	-0.439
angular_range	— – 0.4850 Å⁻¹
current_alpha	0.0000
highest_alpha	1362000.0000
n_real_points	79
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.891; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.999

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	RAB6 GTPASE
formula_weight	18737.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1403

KYKLVFLGEQAVGKTSIITRFMYDTFDNNYQSTIGIDFLSKTLYLDEGPVRLQLWDTAGQERFRSLIPSYIRDSAAAIVVYDITNRQSFENTTKWIQDILNERGKDVIIALVGNKTDLGDLRKVTYEEGMQKAQEYNTMFHETSAKAGHNIKVLFKKTASKL

Source

organism	Plasmodium falciparum
common_name	malaria parasite P. falciparum
ncbi_taxonomy_id	5833
host_organism	Escherichia coli

Entity 2 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	GUANOSINE-5'-DIPHOSPHATE
formula_weight	443.2 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	63

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6. Citations (1)

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length_a	81.200 Å
length_b	81.200 Å
length_c	90.840 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 43 21 2
int_tables_number	96
crystal_system	—

resolution	2.300 Å
resolution_low	9.940 Å
r_factor	—
r_work	0.2140
r_free	0.2460

fit	/app/data/saxs_computation/d5/1d5c/1d5c.fit
pddf	/app/data/pr_computation/d5/1d5c/1d5c.pr.out
profile	/app/data/saxs_computation/d5/1d5c/1d5c.dat

CRYSTAL STRUCTURE OF PLASMODIUM FALCIPARUM RAB6 COMPLEXED WITH GDP

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