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1bpz

HUMAN DNA POLYMERASE BETA COMPLEXED WITH NICKED DNA

Method: X-RAY DIFFRACTION D_max: 72.4 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1bpz
deposition_date	1997-04-14
title	HUMAN DNA POLYMERASE BETA COMPLEXED WITH NICKED DNA
keywords	NUCLEOTIDYLTRANSFERASE, DNA REPAIR, BASE EXCISION REPAIR PATHWAY, 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	23.56 Å
rg_electron	22.94 Å
i0	47983100.00
molecular_weight	47537.0 kDa
excluded_volume	56843 Å³
envelope_volume	72080 Å³
shell_volume	26160 Å³
envelope_diameter	75.3 Å
shell_rg	29.89 Å
envelope_rg	22.73 Å
shape_rg	22.93 Å
total_rg	23.69 Å
total_atoms	3306
n_residues	362
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	72.4 Å
rg_real	23.40 Å
rg_real_error	0.42 Å
i0_real	4.7980e+07
i0_real_error	6.3650e+05
rg_reciprocal	23.44 Å
i0_reciprocal	47980000.0000
total_estimate	0.9054
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	31.7 Å
skewness	0.089
kurtosis	-0.476
angular_range	— – 0.3350 Å⁻¹
current_alpha	0.0000
highest_alpha	4437000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.926; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 1.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	;DNA (5'-D(CPCPGPAPCPCPAPCPGPCPAPTPCPAPGPC)-3') ;
formula_weight	4813.1 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	T
atom_count	3333

CCGACCACGCATCAGC

Entity 2 polymer

description	;DNA (5'-D(GPCPTPGPAPTPGPCPGPTP*G)-3') ;
formula_weight	3405.2 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	P

GCTGATGCGTG

Entity 3 polymer

description	;DNA (5'-D(GPTPCPGP*G)-3') ;
formula_weight	1536.0 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	D

GTCGG

Entity 4 polymer

description	PROTEIN (DNA POLYMERASE BETA)
formula_weight	38241.7 kDa
ec_number	2.7.7.7
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

MSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 5 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	2

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	27

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6. Citations (6)

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length_a	53.535 Å
length_b	78.656 Å
length_c	54.618 Å
angle_alpha	90.00 °
angle_beta	107.54 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.600 Å
resolution_low	20.000 Å
r_factor	0.2430
r_work	—
r_free	—

fit	/app/data/saxs_computation/bp/1bpz/1bpz.fit
pddf	/app/data/pr_computation/bp/1bpz/1bpz.pr.out
profile	/app/data/saxs_computation/bp/1bpz/1bpz.dat

HUMAN DNA POLYMERASE BETA COMPLEXED WITH NICKED 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 (6)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Source

Entity 5 non-polymer

Entity 6 water

6. Citations (6)

7. Files & Curves (10)

Files (7)

Curves (3)