SAXSdb — 9r43

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1. Structure Basics

entry_id	9r43
deposition_date	2025-05-07
last_revision	2025-12-10
title	FAD-dependent oxidoreductase McrA
keywords	Flavin, FAD, natural product, oxidase, mitomycin C, OXIDOREDUCTASE; 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	34.43 Å
rg_electron	33.89 Å
i0	156145000.00
molecular_weight	98187.0 kDa
excluded_volume	121800 Å³
envelope_volume	151160 Å³
shell_volume	36600 Å³
envelope_diameter	105.9 Å
shell_rg	41.12 Å
envelope_rg	33.44 Å
shape_rg	33.87 Å
total_rg	34.47 Å
total_atoms	6923
n_residues	882
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	106.8 Å
rg_real	34.48 Å
rg_real_error	0.59 Å
i0_real	1.5610e+08
i0_real_error	2.2440e+06
rg_reciprocal	34.46 Å
i0_reciprocal	156100000.0000
total_estimate	0.8773
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	30.2 Å
skewness	0.253
kurtosis	-0.834
angular_range	— – 0.2300 Å⁻¹
current_alpha	0.0000
highest_alpha	68990000.0000
n_real_points	47
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.902; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.934; Smooth: 0.760

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Mitomycin radical oxidase
formula_weight	48406.2 kDa
ec_number	1.5.3.-
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	7166

MSTQWGWALEPDQPGYDDARLGLNRAAESRPAYVVEAADEQEVAAAVRLAAEQKRPVGVMATGHGPSVSADDAVLVNTRRMEGVSVDAARATAWIEAGARWRKVLEHTAPHGLAPLNGSSPNVGAVGYLVGGGAGLLGRRFGYAADHVRRLRLVTADGRLRDVTAGTDPDLFWAVRGGKDNFGLVVGMEVDLFPVTRLYGGGLYFAGEATAEVLHAYAEWVRHVPEEMASSVLLVHNPDLPDVPEPLRGRFITHLRIAYSGEPADGEHLVRPLRELGPILLDTVRDMPYAEVGTIHHEPTSMPYVAYDRNVLLSDLTDDAVDIIVALAGPDAGAPFVTELRHFGGAYARPPKVPNCVGGRDAAFSLFTGAVPEAEGLRRRDDLLDRLRPWSTGGTNLNFAGVEDISPASVEAAYTPADFARLRAVKAQYDPDNMFRVNFNIPPAESWT

Source

organism	Streptomyces lavendulae
ncbi_taxonomy_id	1914
host_organism	Escherichia coli

Entity 2 non-polymer

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

Entity 3 non-polymer

description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
formula_weight	238.3 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	16

Entity 5 non-polymer

description	ACETATE ION
formula_weight	59.0 kDa
src_method	syn
entity_count	8

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	243

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6. Citations (1)

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length_a	77.872 Å
length_b	80.490 Å
length_c	163.811 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 2 2 21
int_tables_number	17
crystal_system	—

resolution	2.100 Å
resolution_low	72.340 Å
r_factor	0.2047
r_work	0.2023
r_free	0.2467

fit	/app/data/saxs_computation/r4/9r43/9r43.fit
pddf	/app/data/pr_computation/r4/9r43/9r43.pr.out
profile	/app/data/saxs_computation/r4/9r43/9r43.dat

FAD-dependent oxidoreductase McrA

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