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1d8y

CRYSTAL STRUCTURE OF THE COMPLEX OF DNA POLYMERASE I KLENOW FRAGMENT WITH DNA

Method: X-RAY DIFFRACTION D_max: 89.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1d8y
deposition_date	1999-10-26
title	CRYSTAL STRUCTURE OF THE COMPLEX OF DNA POLYMERASE I KLENOW FRAGMENT WITH DNA
keywords	DNA POLYMERASE I, POLY-D(T), TRANSFERASE-DNA COMPLEX; TRANSFERASE/DNA
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	27.93 Å
rg_electron	27.32 Å
i0	77591800.00
molecular_weight	68630.0 kDa
excluded_volume	85736 Å³
envelope_volume	107530 Å³
shell_volume	32910 Å³
envelope_diameter	95.6 Å
shell_rg	34.74 Å
envelope_rg	27.18 Å
shape_rg	27.33 Å
total_rg	28.01 Å
total_atoms	4822
n_residues	605
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	89.0 Å
rg_real	27.85 Å
rg_real_error	0.53 Å
i0_real	7.7590e+07
i0_real_error	1.0670e+06
rg_reciprocal	27.88 Å
i0_reciprocal	77590000.0000
total_estimate	0.8971
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	34.4 Å
skewness	0.259
kurtosis	-0.388
angular_range	— – 0.2850 Å⁻¹
current_alpha	0.0000
highest_alpha	19470000.0000
n_real_points	58
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.920; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.898

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	D(T)19 OLIGOMER
formula_weight	5734.7 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	B
atom_count	5157

TTTTTTTTTTTTTTTTTTT

Entity 2 polymer

description	DNA POLYMERASE I
formula_weight	68091.7 kDa
ec_number	2.7.7.7
mutation	D355A, E357A
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

MISYDNYVTILDEETLKAWIAKLEKAPVFAFATATDSLDNISANLVGLSFAIEPGVAAYIPVAHDYLDAPDQISRERALELLKPLLEDEKALKVGQNLKYDRGILANYGIELRGIAFDTMLESYILNSVAGRHDMDSLAERWLKHKTITFEEIAGKGKNQLTFNQIALEEAGRYAAEDADVTLQLHLKMWPDLQKHKGPLNVFENIEMPLVPVLSRIERNGVKIDPKVLHNHSEELTLRLAELEKKAHEIAGEEFNLSSTKQLQTILFEKQGIKPLKKTPGGAPSTSEEVLEELALDYPLPKVILEYRGLAKLKSTYTDKLPLMINPKTGRVHTSYHQAVTATGRLSSTDPNLQNIPVRNEEGRRIRQAFIAPEDYVIVSADYSQIELRIMAHLSRDKGLLTAFAEGKDIHRATAAEVFGLPLETVTSEQRRSAKAINFGLIYGMSAFGLARQLNIPRKEAQKYMDLYFERYPGVLEYMERTRAQAKEQGYVETLDGRRLYLPDIKSSNGARRAAAERAAINAPMQGTAADIIKRAMIAVDAWLQAEQPRVRMIMQVHDELVFEVHKDDVDAVAKQIHQLMENCTRLDVPLLVEVGSGENWDQAH

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 3 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	3

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	335

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6. Citations (1)

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length_a	101.880 Å
length_b	101.880 Å
length_c	85.180 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 43
int_tables_number	78
crystal_system	—

resolution	2.080 Å
resolution_low	20.000 Å
r_factor	0.2170
r_work	0.2170
r_free	0.2330

fit	/app/data/saxs_computation/d8/1d8y/1d8y.fit
pddf	/app/data/pr_computation/d8/1d8y/1d8y.pr.out
profile	/app/data/saxs_computation/d8/1d8y/1d8y.dat

CRYSTAL STRUCTURE OF THE COMPLEX OF DNA POLYMERASE I KLENOW FRAGMENT WITH DNA

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

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)