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1d9f

;CRYSTAL STRUCTURE OF THE COMPLEX OF DNA POLYMERASE I KLENOW FRAGMENT WITH DNA TETRAMER CARRYING 2'-O-(3-AMINOPROPYL)-RNA MODIFICATION 5'-D(TT)-AP(U)-D(T)-3' ;

Method: X-RAY DIFFRACTION D_max: 91.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1d9f
deposition_date	1999-10-27
title	;CRYSTAL STRUCTURE OF THE COMPLEX OF DNA POLYMERASE I KLENOW FRAGMENT WITH DNA TETRAMER CARRYING 2'-O-(3-AMINOPROPYL)-RNA MODIFICATION 5'-D(TT)-AP(U)-D(T)-3' ;
keywords	;KLENOW FRAGMENT, 2'-O-AMINOPROPYL NUCLEOTIDES, TRANSFERASE/DNA, RNA COMPLEX, TRANSFERASE-DNA ;; TRANSFERASE/DNA, RNA
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	28.22 Å
rg_electron	27.59 Å
i0	78345100.00
molecular_weight	68821.0 kDa
excluded_volume	85919 Å³
envelope_volume	109940 Å³
shell_volume	33335 Å³
envelope_diameter	95.9 Å
shell_rg	34.95 Å
envelope_rg	27.40 Å
shape_rg	27.60 Å
total_rg	28.27 Å
total_atoms	4835
n_residues	603
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	91.0 Å
rg_real	28.14 Å
rg_real_error	0.50 Å
i0_real	7.8350e+07
i0_real_error	1.0340e+06
rg_reciprocal	28.17 Å
i0_reciprocal	78350000.0000
total_estimate	0.8972
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	35.8 Å
skewness	0.241
kurtosis	-0.418
angular_range	— – 0.2800 Å⁻¹
current_alpha	0.0000
highest_alpha	21990000.0000
n_real_points	57
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.908; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.940

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	;DNA/RNA (5'-D(TPTP)-R((U31)P)-D(T)-3') ;
formula_weight	1230.9 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide/polyribonucleotide hybrid
strand_id	B
atom_count	4934

TTUT

Entity 2 polymer

description	DNA POLYMERASE I
formula_weight	68193.8 kDa
ec_number	2.7.7.7
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

MISYDNYVTILDEETLKAWIAKLEKAPVFAFDTETDSLDNISANLVGLSFAIEPGVAAYIPVAHDYLDAPDQISRERALELLKPLLEDEKALKVGQNLKYDRGILANYGIELRGIAFDTMLESYILNSVAGRHDMDSLAERWLKHKTITFEEIAGKGKNQLTFNQIALEEAGRYAAEDADVTLQLHLKMWPDLQKHKGPLNVFENIEMPLVPVLSRIERNGVKIDPKVLHNHSEELTLRLAELEKKAHEIAGEEFNLSSTKQLQTILFEKQGIKPLKKTPGGAPSTSEEVLEELALDYPLPKVILEYRGLAKLKSTYTDKLPLMINPKTGRVHTSYHQAVTATGRLSSTDPNLQNIPVRNEEGRRIRQAFIAPEDYVIVSADYSQIELRIMAHLSRDKGLLTAFAEGKDIHRATAAEVFGLPLETVTSEQRRSAKAINFGLIYGMSAFGLARQLNIPRKEAQKYMDLYFERYPGVLEYMERTRAQAKEQGYVETLDGRRLYLPDIKSSNGARRAAAERAAINAPMQGTAADIIKRAMIAVDAWLQAEQPRVRMIMQVHDELVFEVHKDDVDAVAKQIHQLMENCTRLDVPLLVEVGSGENWDQAH

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	4

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	38

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6. Citations (1)

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length_a	102.650 Å
length_b	102.650 Å
length_c	86.300 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	3.000 Å
resolution_low	20.000 Å
r_factor	0.2240
r_work	0.2240
r_free	0.2430

fit	/app/data/saxs_computation/d9/1d9f/1d9f.fit
pddf	/app/data/pr_computation/d9/1d9f/1d9f.pr.out
profile	/app/data/saxs_computation/d9/1d9f/1d9f.dat

;CRYSTAL STRUCTURE OF THE COMPLEX OF DNA POLYMERASE I KLENOW FRAGMENT WITH DNA TETRAMER CARRYING 2'-O-(3-AMINOPROPYL)-RNA MODIFICATION 5'-D(TT)-AP(U)-D(T)-3' ;

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)