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1bpy

HUMAN DNA POLYMERASE BETA COMPLEXED WITH GAPPED DNA AND DDCTP

Method: X-RAY DIFFRACTION D_max: 72.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1bpy
deposition_date	1997-04-15
title	HUMAN DNA POLYMERASE BETA COMPLEXED WITH GAPPED DNA AND DDCTP
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	22.76 Å
rg_electron	22.10 Å
i0	47847900.00
molecular_weight	47178.0 kDa
excluded_volume	56254 Å³
envelope_volume	69502 Å³
shell_volume	25809 Å³
envelope_diameter	76.0 Å
shell_rg	29.23 Å
envelope_rg	22.15 Å
shape_rg	22.10 Å
total_rg	22.86 Å
total_atoms	3276
n_residues	356
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	72.8 Å
rg_real	22.62 Å
rg_real_error	0.43 Å
i0_real	4.7850e+07
i0_real_error	5.5060e+05
rg_reciprocal	22.66 Å
i0_reciprocal	47850000.0000
total_estimate	0.8920
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	29.8 Å
skewness	0.127
kurtosis	-0.433
angular_range	— – 0.3500 Å⁻¹
current_alpha	0.0000
highest_alpha	5580000.0000
n_real_points	67
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.873; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.984

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	;DNA (5'-D(CPCPGPAPCPGPGPCPGPCPAPTPCPAPGPC)-3') ;
formula_weight	4869.2 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	T
atom_count	3597

CCGACGGCGCATCAGC

Entity 2 polymer

description	;DNA (5'-D(GPCPTPGPAPTPGPCPGPDOC)-3') ;
formula_weight	3045.0 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	P

GCTGATGCGC

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	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	2

Entity 7 non-polymer

description	;2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE ;
formula_weight	451.2 kDa
src_method	syn
entity_count	1

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	321

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6. Citations (6)

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length_a	50.543 Å
length_b	79.817 Å
length_c	54.942 Å
angle_alpha	90.00 °
angle_beta	107.11 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.200 Å
resolution_low	20.000 Å
r_factor	0.2270
r_work	0.2320
r_free	0.3300

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

HUMAN DNA POLYMERASE BETA COMPLEXED WITH GAPPED DNA AND DDCTP

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 (8)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Source

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 water

6. Citations (6)

7. Files & Curves (10)

Files (7)

Curves (3)