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1dnp

STRUCTURE OF DEOXYRIBODIPYRIMIDINE PHOTOLYASE

Method: X-RAY DIFFRACTION D_max: 104.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1dnp
deposition_date	1995-07-03
title	STRUCTURE OF DEOXYRIBODIPYRIMIDINE PHOTOLYASE
keywords	DNA REPAIR, ELECTRON TRANSFER, EXCITATION ENERGY TRANSFER, LYASE, CARBON-CARBON, LYASE (CARBON-CARBON); LYASE (CARBON-CARBON)
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	31.91 Å
rg_electron	31.33 Å
i0	193440000.00
molecular_weight	109150.0 kDa
excluded_volume	135530 Å³
envelope_volume	165070 Å³
shell_volume	43100 Å³
envelope_diameter	111.0 Å
shell_rg	38.87 Å
envelope_rg	31.45 Å
shape_rg	31.27 Å
total_rg	32.11 Å
total_atoms	7708
n_residues	938
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	104.9 Å
rg_real	31.93 Å
rg_real_error	0.76 Å
i0_real	1.9340e+08
i0_real_error	3.1750e+06
rg_reciprocal	31.92 Å
i0_reciprocal	193400000.0000
total_estimate	0.8871
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	35.7 Å
skewness	0.398
kurtosis	-0.286
angular_range	— – 0.2500 Å⁻¹
current_alpha	0.0000
highest_alpha	49890000.0000
n_real_points	51
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.865; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.934

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	DNA PHOTOLYASE
formula_weight	53601.6 kDa
ec_number	4.1.99.3
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	8081

TTHLVWFRQDLRLHDNLALAAACRNSSARVLALYIATPRQWATHNMSPRQAELINAQLNGLQIALAEKGIPLLFREVDDFVASVEIVKQVCAENSVTHLFYNYQYEVNERARDVEVERALRNVVCEGFDDSVILPPGAVMTGNHEMYKVFTPFKNAWLKRLREGMPECVAAPKVRSSGSIEPSPSITLNYPRQSFDTAHFPVEEKAAIAQLRQFCQNGAGEYEQQRDFPAVEGTSRLSASLATGGLSPRQCLHRLLAEQPQALDGGAGSVWLNELIWREFYRHLITYHPSLCKHRPFIAWTDRVQWQSNPAHLQAWQEGKTGYPIVDAAMRQLNSTGWMHNRLRMITASFLVKDLLIDWREGERYFMSQLIDGDLAANNGGWQWAASTGTDAAPYFRIFNPTTQGEKFDHEGEFIRQWLPELRDVPGKVVHEPWKWAQKAGVTLDYPQPIVEHKEARVQTLAAYEAARKGK

Entity 2 non-polymer

description	FLAVIN-ADENINE DINUCLEOTIDE
formula_weight	785.5 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	5,10-METHENYL-6,7,8-TRIHYDROFOLIC ACID
formula_weight	457.4 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	373

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6. Citations (2)

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length_a	62.600 Å
length_b	72.200 Å
length_c	58.500 Å
angle_alpha	99.10 °
angle_beta	101.50 °
angle_gamma	72.00 °
z_pdb	2

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.300 Å
resolution_low	10.000 Å
r_factor	0.1720
r_work	0.1720
r_free	0.2460

fit	/app/data/saxs_computation/dn/1dnp/1dnp.fit
pddf	/app/data/pr_computation/dn/1dnp/1dnp.pr.out
profile	/app/data/saxs_computation/dn/1dnp/1dnp.dat