← Back to search

1cvr

Crystal structure of the Arg specific cysteine proteinase gingipain R (RGPB)

Method: X-RAY DIFFRACTION D_max: 71.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	1cvr
deposition_date	1999-08-24
title	Crystal structure of the Arg specific cysteine proteinase gingipain R (RGPB)
keywords	CASPASES, CYSTEINE PROTEINASE, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/HYDROLASE INHIBITOR
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	22.28 Å
rg_electron	21.21 Å
i0	39786400.00
molecular_weight	48440.0 kDa
excluded_volume	60396 Å³
envelope_volume	68544 Å³
shell_volume	26283 Å³
envelope_diameter	76.3 Å
shell_rg	28.88 Å
envelope_rg	21.61 Å
shape_rg	21.19 Å
total_rg	22.18 Å
total_atoms	3387
n_residues	432
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	71.9 Å
rg_real	22.19 Å
rg_real_error	0.52 Å
i0_real	3.9790e+07
i0_real_error	5.5150e+05
rg_reciprocal	22.22 Å
i0_reciprocal	39790000.0000
total_estimate	0.8075
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	28.3 Å
skewness	0.271
kurtosis	-0.230
angular_range	— – 0.3550 Å⁻¹
current_alpha	0.0000
highest_alpha	9963000.0000
n_real_points	67
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.834; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.000

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (5)

Entity 1 polymer

description	GINGIPAIN R
formula_weight	47932.8 kDa
ec_number	3.4.22.37
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3709

YTPVEEKENGRMIVIVAKKYEGDIKDFVDWKNQRGLRTEVKVAEDIASPVTANAIQQFVKQEYEKEGNDLTYVLLVGDHKDIPAKITPGIKSDQVYGQIVGNDHYNEVFIGRFSCESKEDLKTQIDRTIHYERNITTEDKWLGQALCIASAEGGPSADNGESDIQHENVIANLLTQYGYTKIIKCYDPGVTPKNIIDAFNGGISLVNYTGHGSETAWGTSHFGTTHVKQLTNSNQLPFIFDVACVNGDFLFSMPCFAEALMRAQKDGKPTGTVAIIASTIDQYWAPPMRGQDEMNEILCEKHPNNIKRTFGGVTMNGMFAMVEKYKKDGENMLDTWTVFGDPSLLVRTLVPTEMQVTAPANISASAQTFEVACDYNGAIATLSDDGDMVGTAIVKDGKAIIKLNESIADETNLTLTVVGYNKVTVIKDVKVEGTS

Source

organism	Porphyromonas gingivalis
ncbi_taxonomy_id	837

Entity 2 non-polymer

description	D-phenylalanyl-N-[(3S)-6-carbamimidamido-1-chloro-2-oxohexan-3-yl]-L-phenylalaninamide
formula_weight	501.0 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	6

Entity 4 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	322

▶

6. Citations (1)

▶

length_a	51.930 Å
length_b	79.920 Å
length_c	99.820 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	2.000 Å
resolution_low	15.000 Å
r_factor	—
r_work	0.1630
r_free	0.2070

fit	/app/data/saxs_computation/cv/1cvr/1cvr.fit
pddf	/app/data/pr_computation/cv/1cvr/1cvr.pr.out
profile	/app/data/saxs_computation/cv/1cvr/1cvr.dat