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1dd9

STRUCTURE OF THE DNAG CATALYTIC CORE

Method: X-RAY DIFFRACTION D_max: 79.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1dd9
deposition_date	1999-11-09
title	STRUCTURE OF THE DNAG CATALYTIC CORE
keywords	TOPRIM, 3-HELIX BUNDLE, DNA-BINDING PROTEIN, RNA POLYMERASE, REPLICATION PROTEIN, PRIMASE, TRANSFERASE; TRANSFERASE
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	23.58 Å
rg_electron	22.88 Å
i0	21752300.00
molecular_weight	34990.0 kDa
excluded_volume	43567 Å³
envelope_volume	52431 Å³
shell_volume	20448 Å³
envelope_diameter	83.3 Å
shell_rg	28.44 Å
envelope_rg	23.17 Å
shape_rg	22.89 Å
total_rg	23.56 Å
total_atoms	2459
n_residues	310
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	79.9 Å
rg_real	23.74 Å
rg_real_error	0.52 Å
i0_real	2.1750e+07
i0_real_error	2.4070e+05
rg_reciprocal	23.70 Å
i0_reciprocal	21750000.0000
total_estimate	0.8565
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.7 Å
skewness	0.543
kurtosis	-0.148
angular_range	— – 0.3350 Å⁻¹
current_alpha	0.0000
highest_alpha	5651000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.779; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.877; Smooth: 0.919

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	DNA PRIMASE
formula_weight	38222.3 kDa
ec_number	2.7.7.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2693

MRGSHHHHHHGSGSMHQRQTLYQLMDGLNTFYQQSLQQPVATSARQYLEKRGLSHEVIARFAIGFAPPGWDNVLKRFGGNPENRQSLIDAGMLVTNDQGRSYDRFRERVMFPIRDKRGRVIGFGGRVLGNDTPKYLNSPETDIFHKGRQLYGLYEAQQDNAEPNRLLVVEGYMDVVALAQYGINYAVASLGTSTTADHIQLLFRATNNVICCYDGDRAGRDAAWRALETALPYMTDGRQLRFMFLPDGEDPDTLVRKEGKEAFEARMEQAMPLSAFLFNSLMPQVDLSTPDGRARLSTLALPLISQVPGETLRIYLRQELGNKLGILDDSQLERLMPK

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 2 non-polymer

description	STRONTIUM ION
formula_weight	87.6 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	234

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6. Citations (1)

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length_a	38.340 Å
length_b	57.870 Å
length_c	148.450 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	1.600 Å
resolution_low	20.000 Å
r_factor	—
r_work	0.2310
r_free	0.2760

fit	/app/data/saxs_computation/dd/1dd9/1dd9.fit
pddf	/app/data/pr_computation/dd/1dd9/1dd9.pr.out
profile	/app/data/saxs_computation/dd/1dd9/1dd9.dat

STRUCTURE OF THE DNAG CATALYTIC CORE

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