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1e1d

Hybrid Cluster Protein from Desulfovibrio vulgaris

Method: X-RAY DIFFRACTION D_max: 80.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1e1d
deposition_date	2000-05-02
title	Hybrid Cluster Protein from Desulfovibrio vulgaris
keywords	OXIDOREDUCTASE, HYBRID CLUSTER, CUBANE, IRON SULFUR, PRISMANE, FUSCOREDOXIN; OXIDOREDUCTASE
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	24.30 Å
rg_electron	23.47 Å
i0	59698000.00
molecular_weight	60672.0 kDa
excluded_volume	76062 Å³
envelope_volume	89156 Å³
shell_volume	30810 Å³
envelope_diameter	83.9 Å
shell_rg	31.49 Å
envelope_rg	23.86 Å
shape_rg	23.53 Å
total_rg	24.15 Å
total_atoms	4234
n_residues	553
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	80.7 Å
rg_real	24.21 Å
rg_real_error	0.50 Å
i0_real	5.9700e+07
i0_real_error	7.6430e+05
rg_reciprocal	24.23 Å
i0_reciprocal	59700000.0000
total_estimate	0.8800
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	78.2 Å
skewness	0.286
kurtosis	-0.308
angular_range	— – 0.3250 Å⁻¹
current_alpha	0.0000
highest_alpha	14750000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.813; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.998

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	HYDROXYLAMINE REDUCTASE
formula_weight	60228.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4649

MFCFQCQETAKNTGCTVKGMCGKPEETANLQDLLIFVLRGIAIYGEKLKELGQPDRSNDDFVLQGLFATITNANWDDARFEAMISEGLARRDKLRNAFLAVYKAKNGKDFSEPLPEAATWTGDSTAFAEKAKSVGILATENEDVRSLRELLIIGLKGVAAYAEHAAVLGFRKTEIDEFMLEALASTTKDLSVDEMVALVMKGRRMAVTTMALLDEANTTTYGNPEITQVNIGVGKNPGILISGHDLKDMAELLKQTEGTGVDVYTHGEMLPANYYPAFKKYPHFVGNYGGSWWQQNPEFESFNGPILLTTNCLVPLKKENTYLDRLYTTGVVGYEGAKHIADRPAGGAKDFSALIAQAKKCPPPVEIETGSIVGGFAHHQVLALADKVVEAVKSGAIKRFVVMAGCDGRQKSRSYYTEVAENLPKDTVILTAGCAKYRYNKLNLGDIGGIPRVLDAGQCNDSYSLAVIALKLKEVFGLDDINDLPVSYDIAWYEQKAVAVLLALLFLGVKGIRLGPTLPAFLSPNVAKVLVENFNIKPIGTVQDDIAAMMAGK

Source

organism	DESULFOVIBRIO VULGARIS
ncbi_taxonomy_id	881
host_organism	DESULFOVIBRIO VULGARIS

Entity 2 non-polymer

description	IRON/SULFUR/OXYGEN HYBRID CLUSTER
formula_weight	367.6 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	IRON/SULFUR CLUSTER
formula_weight	351.6 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	415

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6. Citations (1)

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length_a	64.500 Å
length_b	65.500 Å
length_c	155.200 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	1.720 Å
resolution_low	12.000 Å
r_factor	—
r_work	0.1710
r_free	0.2080

fit	/app/data/saxs_computation/e1/1e1d/1e1d.fit
pddf	/app/data/pr_computation/e1/1e1d/1e1d.pr.out
profile	/app/data/saxs_computation/e1/1e1d/1e1d.dat

Hybrid Cluster Protein from Desulfovibrio vulgaris

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