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1clq

CRYSTAL STRUCTURE OF A REPLICATION FORK DNA POLYMERASE EDITING COMPLEX AT 2.7 A RESOLUTION

Method: X-RAY DIFFRACTION D_max: 105.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1clq
deposition_date	1999-04-30
title	CRYSTAL STRUCTURE OF A REPLICATION FORK DNA POLYMERASE EDITING COMPLEX AT 2.7 A RESOLUTION
keywords	DNA POLYMERASE, GP43, PROOFREADING, EDITING, REPLICATION, 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	33.02 Å
rg_electron	32.15 Å
i0	208109000.00
molecular_weight	112430.0 kDa
excluded_volume	139380 Å³
envelope_volume	185830 Å³
shell_volume	47211 Å³
envelope_diameter	113.1 Å
shell_rg	40.02 Å
envelope_rg	31.71 Å
shape_rg	32.15 Å
total_rg	32.78 Å
total_atoms	7885
n_residues	926
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	105.5 Å
rg_real	32.76 Å
rg_real_error	0.63 Å
i0_real	2.0810e+08
i0_real_error	3.3720e+06
rg_reciprocal	32.88 Å
i0_reciprocal	208100000.0000
total_estimate	0.8965
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	44.0 Å
skewness	0.063
kurtosis	-0.532
angular_range	— – 0.2400 Å⁻¹
current_alpha	0.0000
highest_alpha	22570000.0000
n_real_points	49
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.890; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.989

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	;DNA (5'-D(GPCPGPGPAPAPCPTPAPCP*T)-3') ;
formula_weight	3358.2 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	E
atom_count	8106

GCGGAACTACT

Entity 2 polymer

description	;DNA (5'-D(APGPTPAPGPTPTPCPCPGPCPG)-3') ;
formula_weight	3678.4 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	D

AGTAGTTCCGCG

Entity 3 polymer

description	PROTEIN (DNA POLYMERASE)
formula_weight	104743.2 kDa
ec_number	2.7.7.7
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

MKEFYLTVEQIGDSIFERYIDSNGRERTREVEYKPSLFAHCPESQATKYFDIYGKPCTRKLFANMRDASQWIKRMEDIGLEALGMDDFKLAYLSDTYNYEIKYDHTKIRVANFDIEVTSPDGFPEPSQAKHPIDAITHYDSIDDRFYVFDLLNSPYGNVEEWSIEIAAKLQEQGGDEVPSEIIDKIIYMPFDNEKELLMEYLNFWQQKTPVILTGWNVESFDIPYVYNRIKNIFGESTAKRLSPHRKTRVKVIENMYGSREIITLFGISVLDYIDLYKKFSFTNQPSYSLDYISEFELNVGKLKYDGPISKLRESNHQRYISYNIIDVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVFSPIKTWDAIIFNSLKEQNKVIPQGRSHPVQPYPGAFVKEPIPNRYKYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFVLYGDTDSIYVSADKIIDKVGESKFRDTNHWVDFLDKFARERMEPAIDRGFREMCEYMNNKQHLMFMDREAIAGPPLGSKGIGGFWTGKKRYALNVWDMEGTRYAEPKLKIMGLETQKSSTPKAVQKALKECIRRMLQEGEESLQEYFKEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPKCPFHIRGILTYNRAIKGNIDAPQVVEGEKVYVLPLREGNPFGDKCIAWPSGTEITDLIKDDVLHWMDYTVLLEKTFIKPLEGFTSAAKLDYEKKASLFDMFDF

Source

organism	Enterobacteria phage RB69
ncbi_taxonomy_id	12353
host_organism	Escherichia coli

Entity 4 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	9

Entity 5 non-polymer

description	GUANOSINE-5'-DIPHOSPHATE
formula_weight	443.2 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	221

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6. Citations (1)

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length_a	209.740 Å
length_b	209.740 Å
length_c	114.250 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	9

space_group	H 3
int_tables_number	146
crystal_system	—

resolution	2.700 Å
resolution_low	40.000 Å
r_factor	0.2300
r_work	0.2300
r_free	0.2840

fit	/app/data/saxs_computation/cl/1clq/1clq.fit
pddf	/app/data/pr_computation/cl/1clq/1clq.pr.out
profile	/app/data/saxs_computation/cl/1clq/1clq.dat

CRYSTAL STRUCTURE OF A REPLICATION FORK DNA POLYMERASE EDITING COMPLEX AT 2.7 A RESOLUTION

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 (6)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)