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1d5a

CRYSTAL STRUCTURE OF AN ARCHAEBACTERIAL DNA POLYMERASE D.TOK. DEPOSITION OF SECOND NATIVE STRUCTURE AT 2.4 ANGSTROM

Method: X-RAY DIFFRACTION D_max: 97.5 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1d5a
deposition_date	1999-10-06
title	CRYSTAL STRUCTURE OF AN ARCHAEBACTERIAL DNA POLYMERASE D.TOK. DEPOSITION OF SECOND NATIVE STRUCTURE AT 2.4 ANGSTROM
keywords	DNA POLYMERASE, THERMOSTABLE, EXONUCLEASE, RBD DOMAIN, TRANSFERASE; TRANSFERASE
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	31.44 Å
rg_electron	30.45 Å
i0	115388000.00
molecular_weight	85666.0 kDa
excluded_volume	107590 Å³
envelope_volume	144800 Å³
shell_volume	39416 Å³
envelope_diameter	98.8 Å
shell_rg	37.90 Å
envelope_rg	29.82 Å
shape_rg	30.44 Å
total_rg	31.17 Å
total_atoms	6039
n_residues	733
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	97.5 Å
rg_real	31.28 Å
rg_real_error	0.55 Å
i0_real	1.1540e+08
i0_real_error	1.8130e+06
rg_reciprocal	31.35 Å
i0_reciprocal	115400000.0000
total_estimate	0.9086
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	41.0 Å
skewness	0.115
kurtosis	-0.602
angular_range	— – 0.2500 Å⁻¹
current_alpha	0.0000
highest_alpha	25940000.0000
n_real_points	51
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.954; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.949

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	PROTEIN (DNA POLYMERASE)
formula_weight	84906.0 kDa
ec_number	2.7.7.7
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6144

MILDADYITEDGKPVIRVFKKEKGEFKIDYDRDFEPYIYALLKDDSAIEDIKKITAERHGTTVRVTRAERVKKKFLGRPVEVWKLYFTHPQDVPAIRDKIREHPAVVDIYEYDIPFAKRYLIDRGLIPMEGDEELRMLAFDIETLAHAGAAAGAGPILMISYADEEGARVITWKNIDLPYVESVSTEKEMIKRFLKVIQEKDPDVLITYNGDNFDFAYLKKRSEMLGVKFILGRDGSEPKIQRMGDRFAVEVKGRIHFDLYPVIRRTINLPTYTLETVYEPVFGQPAEKVYAEEIAEAWASGEGLERVARYSMEDAKATYELGKEFFPMEAQLSRLVGQSLWDVSRSSTGNLVEWFLLRKAYERNDVAPNKPDERELARRTESYAGGYVKEPEKGLWENIVYLDYKSLYPSIIITHNVSPDTLNREGCREYDVAPQVGHRFCKDFPGFIPSLLGDLLEERQKVKKKMKATVDPIERKLLDYRQRAIKILANSYYGYYAYANARWYCRECAESVTAWGRQYIETTMREIEEKFGFKVLYADTDGFFATIPGADAETVKNKAKEFLNYINPRLPGLLELEYEGFYRRGFFVTKKKYAVIDEEDKITTRGLEIVRRDWSEIAKETQARVLEAILKHGDVEEAVRIVKEVTEKLSRHEVPPEKLVIYEAGPHVAAAATVISYIVLKGPGRVGDRAIPFDEFDPAKHRYDAEYYIENQVLPAVERILRAFGYRKEDLR

Source

organism	Desulfurococcus sp. Tok
ncbi_taxonomy_id	108142
host_organism	Escherichia coli

Entity 2 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	9

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	105

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6. Citations (1)

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length_a	64.800 Å
length_b	107.600 Å
length_c	153.200 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.400 Å
resolution_low	50.000 Å
r_factor	0.2525
r_work	0.2525
r_free	0.2989

fit	/app/data/saxs_computation/d5/1d5a/1d5a.fit
pddf	/app/data/pr_computation/d5/1d5a/1d5a.pr.out
profile	/app/data/saxs_computation/d5/1d5a/1d5a.dat

CRYSTAL STRUCTURE OF AN ARCHAEBACTERIAL DNA POLYMERASE D.TOK. DEPOSITION OF SECOND NATIVE STRUCTURE AT 2.4 ANGSTROM

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