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1bky

VACCINIA METHYLTRANSFERASE VP39 COMPLEXED WITH M1CYT AND S-ADENOSYLHOMOCYSTEINE

Method: X-RAY DIFFRACTION D_max: 61.6 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1bky
deposition_date	1998-07-13
title	VACCINIA METHYLTRANSFERASE VP39 COMPLEXED WITH M1CYT AND S-ADENOSYLHOMOCYSTEINE
keywords	;METHYLATED CYTOSINE, METHYLTRANSFERASE, RNA CAP ANALOG, POLY(A) POLYMERASE, VACCINIA, MRNA PROCESSING, TRANSCRIPTION, COMPLEX (TRANSFERASE-RNA CAP ANALOG) ;; MRNA PROCESSING
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	20.19 Å
rg_electron	19.03 Å
i0	18726000.00
molecular_weight	34526.0 kDa
excluded_volume	43901 Å³
envelope_volume	49493 Å³
shell_volume	21263 Å³
envelope_diameter	63.4 Å
shell_rg	25.72 Å
envelope_rg	19.26 Å
shape_rg	19.03 Å
total_rg	19.97 Å
total_atoms	2967
n_residues	291
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	61.6 Å
rg_real	20.07 Å
rg_real_error	0.33 Å
i0_real	1.8730e+07
i0_real_error	2.4330e+05
rg_reciprocal	20.09 Å
i0_reciprocal	18730000.0000
total_estimate	0.9031
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	25.5 Å
skewness	0.127
kurtosis	-0.491
angular_range	— – 0.3950 Å⁻¹
current_alpha	0.0000
highest_alpha	4736000.0000
n_real_points	71
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.920; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.994

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	VP39
formula_weight	35921.4 kDa
ec_number	2.7.7.19
mutation	C-TERMINAL DELETION OF 26 RESIDUES
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3321

MDVVSLDKPFMYFEEIDNELDYEPESANEVAKKLPYQGQLKLLLGELFFLSKLQRHGILDGATVVYIGSAPGTHIRYLRDHFYNLGVIIKWMLIDGRHHDPILNGLRDVTLVTRFVDEEYLRSIKKQLHPSKIILISDVRSKRGGNEPSTADLLSNYALQNVMISILNPVASSLKWRCPFPDQWIKDFYIPHGNKMLQPFAPSYSAEMRLLSIYTGENMRLTRVTKSDAVNYEKKMYYLNKIVRNKVVVNFDYPNQEYDYFHMYFMLRTVYCNKTFPTTKAKVLFLQQSIFRFLNIPTTSTEKVSHE

Source

organism	Vaccinia virus
ncbi_taxonomy_id	10245
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	S-ADENOSYL-L-HOMOCYSTEINE
formula_weight	384.4 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	1-METHYLCYTOSINE
formula_weight	125.1 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	118

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6. Citations (1)

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length_a	84.500 Å
length_b	67.210 Å
length_c	79.560 Å
angle_alpha	90.00 °
angle_beta	117.30 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.000 Å
resolution_low	8.000 Å
r_factor	0.2270
r_work	0.2270
r_free	0.2610

fit	/app/data/saxs_computation/bk/1bky/1bky.fit
pddf	/app/data/pr_computation/bk/1bky/1bky.pr.out
profile	/app/data/saxs_computation/bk/1bky/1bky.dat

VACCINIA METHYLTRANSFERASE VP39 COMPLEXED WITH M1CYT AND S-ADENOSYLHOMOCYSTEINE

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