SAXSdb — 9pzj

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1. Structure Basics

entry_id	9pzj
deposition_date	2025-08-11
title	Benzylsuccinate synthase alpha-beta-gamma complex with bound toluene and fumarate
keywords	Benzylsuccinate Synthase, Glycyl Radical Enzyme, FeS cluster, toluene, fumarate, LYASE; LYASE
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	42.40 Å
rg_electron	42.30 Å
i0	776125000.00
molecular_weight	224040.0 kDa
excluded_volume	277380 Å³
envelope_volume	335230 Å³
shell_volume	64901 Å³
envelope_diameter	152.6 Å
shell_rg	48.29 Å
envelope_rg	42.35 Å
shape_rg	42.29 Å
total_rg	42.55 Å
total_atoms	15687
n_residues	1961
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	140.3 Å
rg_real	42.48 Å
rg_real_error	1.55 Å
i0_real	7.7610e+08
i0_real_error	1.5000e+07
rg_reciprocal	42.40 Å
i0_reciprocal	776100000.0000
total_estimate	0.8797
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	41.7 Å
skewness	0.355
kurtosis	-0.561
angular_range	— – 0.1850 Å⁻¹
current_alpha	0.0000
highest_alpha	151800000.0000
n_real_points	38
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.852; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.893

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	benzylsuccinate synthase alpha chain
formula_weight	99117.1 kDa
ec_number	4.1.99.11
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,D
atom_count	15700

MNDIVSAKVLEYKGKKLNFTPEDPAEETIPADELHEHLQKPSTARTKRLKERCRWKHASAGEFIEKSVTAGIERMRYLTEAHKASEGKPEAIRRALGLANVLNKSTLVLQEDEFIVGYHAEDPNMFPLYPELSHMAVQDYLRSDYSPQPADEAAAINEYWKPHSLQSKCQPYFDPADLGRMYQVSSMEAPSFASGYNSIVPPYETVLEDGLLARIKLAEKHIAEAQADMSTFPWNGTKGLDNIAKIDNWKAMVIACKAVISWARRQGRLCKIVAENFETDPKRQAELLEIADICQRIPAEPCKGLKDAMQAKFFTFLICHAIERYASGYAQKEDTLLWPYYKASVVDKKFQPMSHMDAVELVEMERLKISEHGAGKSRAYREIFPGSNDLFILTVGGTNAKGEDACNDMTDAILEAAKRIRTAEPSIVFRYSKKNREKTLRWVFECIRDGLGYPSIKHDEIGTEQMKEYAKFSLNGNGATDEEAHNWVNVLCMSPGIHGRRKTQKTRSEGGGSIFPAKLLEISLNDGYDWSYADMQLGPKTGDLSSLKSFEDVWEAFRKQYQYAINLCISTKDVSRYFEQRFLQMPFVSAIDDGCMELGMDACALSEQPNGWHNPITTIVAANSLVAIKKLVFEEKKYTLEQLSQALKANWEGFEEMRVDFKRAPKWGNDDDYADGIITRFYEEIIGGEMRKITNYSGGPVMPTGQAVGLYMEVGSRTGPTPDGRFGGEAADDGGISPYMGTDKKGPTAVLRSVSKVQKNQKGNLLNQRLSVPIMRSKHGFEIWNSYIKTWHDLNIDHVQFNVVSTDEMRAAQREPEKHHDLIVRVSGYSARFVDIPTYGQNTIIARQEQDFSASDLEFLNVEISGTGSGSSHHHHHH

Source

organism	Thauera aromatica
ncbi_taxonomy_id	59405
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	benzylsuccinate synthase beta chain
formula_weight	11730.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,E

MASSHHHHHHDPTTENLYFQGSEGSNMETGQNLQNQPHTEVGTARPCRSCKWQTPDPTDPHRGQCTANRHAMGGVWKRWLRDVENTTCSRHEEGKLSFRDHV

Source

organism	Thauera aromatica
ncbi_taxonomy_id	59405
host_organism	Escherichia coli BL21(DE3)

Entity 3 polymer

description	benzylsuccinate synthase gamma chain
formula_weight	6865.7 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,F

MGTTTCKQCANFFPVPKDADDYEAGKADCVREKEDEKGKYWLSKPIFENSAQCEAFQTKR

Source

organism	Thauera aromatica
ncbi_taxonomy_id	59405
host_organism	Escherichia coli BL21(DE3)

Entity 4 non-polymer

description	FUMARIC ACID
formula_weight	116.1 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	TOLUENE
formula_weight	92.1 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	nat
entity_count	2

Entity 7 non-polymer

description	IRON/SULFUR CLUSTER
formula_weight	351.6 kDa
src_method	syn
entity_count	4

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	13

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6. Citations (1)

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length_a	146.396 Å
length_b	118.535 Å
length_c	124.929 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 2
int_tables_number	18
crystal_system	—

resolution	2.900 Å
resolution_low	33.680 Å
r_factor	0.2128
r_work	0.2118
r_free	0.2461

fit	/app/data/saxs_computation/pz/9pzj/9pzj.fit
pddf	/app/data/pr_computation/pz/9pzj/9pzj.pr.out
profile	/app/data/saxs_computation/pz/9pzj/9pzj.dat

Benzylsuccinate synthase alpha-beta-gamma complex with bound toluene and fumarate

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

5. Entities & Polymer Info (8)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)