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1dgs

CRYSTAL STRUCTURE OF NAD+-DEPENDENT DNA LIGASE FROM T. FILIFORMIS

Method: X-RAY DIFFRACTION D_max: 168.9 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1dgs
deposition_date	1999-11-25
title	CRYSTAL STRUCTURE OF NAD+-DEPENDENT DNA LIGASE FROM T. FILIFORMIS
keywords	AMP COMPLEX, NAD+-DEPENDENT, LIGASE; LIGASE
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	52.40 Å
rg_electron	53.04 Å
i0	264646000.00
molecular_weight	133880.0 kDa
excluded_volume	167620 Å³
envelope_volume	268040 Å³
shell_volume	45224 Å³
envelope_diameter	180.5 Å
shell_rg	49.96 Å
envelope_rg	52.29 Å
shape_rg	52.94 Å
total_rg	53.28 Å
total_atoms	9432
n_residues	1162
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	168.9 Å
rg_real	52.98 Å
rg_real_error	1.84 Å
i0_real	2.6460e+08
i0_real_error	4.8010e+06
rg_reciprocal	51.89 Å
i0_reciprocal	264200000.0000
total_estimate	0.7496
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	50.7 Å
skewness	0.526
kurtosis	-0.573
angular_range	— – 0.1500 Å⁻¹
current_alpha	0.0000
highest_alpha	8328000.0000
n_real_points	31
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.641; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.789; Smooth: 0.030

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	DNA LIGASE
formula_weight	75998.0 kDa
ec_number	6.5.1.2
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	9674

MTREEARRRINELRDLIRYHNYRYYVLADPEISDAEYDRLLRELKELEERFPEFKSPDSPTEQVGARPLEPTFRPVRHPTRMYSLDNAFTYEEVLAFEERLEREAEAPSLYTVEHKVDGLSVLYYEEGVWSTGSGDGEVGEEVTQNLLTIPTIPRRLKGVPDRLEVRGEVYMPIEAFLRLNEELEERGEKVFKNPRNAAAGSLRQKDPRVTAKRGLRATFYALGLGLGLEESGLKSQYELLLWLKEKGFPVEHCYEKALGAEGVEEVYRRGLAQRHALPFEADGVVLKLDDLTLWGELGYTARAPRFALAYKFPAEEKETRLLDVVFQVGRTGRVTPVGVLEPVFIEGSEVSRVTLHNESYIEELDIRIGDWVLVHKAGGVIPEVLRVLKERRTGKERPIRWPEACPECGHRLVKEGKVHRCPNPLCPAKRFEAIRHYASRKAMDIEGLGEKLIERLLEKGLVRDVADLYHLRKEDLLGLERMGEKSAQNLLRQIEESKHRGLERLLYALGLPGVGEVLARNLARRFGTMDRLLEASLEELIEVEEVGELTARAILETLKDPAFRDLVRRLKEAGVSMESKEEVSDLLSGLTFVLTGELSRPREEVKALLGRLGAKVTDSVSRKTSYLVVGENPGSKLEKARALGVAVLTEEEFWRFLKEKGAPVPA

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	ADENOSINE MONOPHOSPHATE
formula_weight	347.2 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	242

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6. Citations (1)

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length_a	89.210 Å
length_b	117.330 Å
length_c	97.480 Å
angle_alpha	90.00 °
angle_beta	115.09 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.900 Å
resolution_low	20.000 Å
r_factor	—
r_work	0.2280
r_free	0.2980

fit	/app/data/saxs_computation/dg/1dgs/1dgs.fit
pddf	/app/data/pr_computation/dg/1dgs/1dgs.pr.out
profile	/app/data/saxs_computation/dg/1dgs/1dgs.dat

CRYSTAL STRUCTURE OF NAD+-DEPENDENT DNA LIGASE FROM T. FILIFORMIS

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