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9scf

Fe(II)-2-oxoglutarate-dependent Pseudomonas savastanoi pv phaseolicola 1449B in complex with 2-oxoglutarate

Method: X-RAY DIFFRACTION D_max: 60.5 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9scf
deposition_date	2025-08-10
last_revision	2026-03-18
title	Fe(II)-2-oxoglutarate-dependent Pseudomonas savastanoi pv phaseolicola 1449B in complex with 2-oxoglutarate
keywords	oxodoreductase, Iron, 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	20.34 Å
rg_electron	19.18 Å
i0	25334200.00
molecular_weight	38031.0 kDa
excluded_volume	47337 Å³
envelope_volume	54460 Å³
shell_volume	22897 Å³
envelope_diameter	61.5 Å
shell_rg	26.40 Å
envelope_rg	19.49 Å
shape_rg	19.16 Å
total_rg	20.17 Å
total_atoms	2675
n_residues	335
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	60.5 Å
rg_real	20.18 Å
rg_real_error	0.28 Å
i0_real	2.5330e+07
i0_real_error	3.0690e+05
rg_reciprocal	20.21 Å
i0_reciprocal	25330000.0000
total_estimate	0.7119
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	26.8 Å
skewness	0.073
kurtosis	-0.509
angular_range	— – 0.3900 Å⁻¹
current_alpha	0.0000
highest_alpha	6895000.0000
n_real_points	71
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.938; Stabil: 1.000; Sysdev: 0.193; Positv: 1.000; Valcen: 0.974; Smooth: 0.881

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	2-oxoglutarate-dependent ethylene/succinate-forming enzyme
formula_weight	38110.2 kDa
ec_number	1.13.12.19,1.14.20.7
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2981

MTNLQTFELPTEVIGSAADISLGRALIQAWQKDGILQIKTDSEQNRKTQEAMAASKQFCKEPLTFKSSCVSDLTYSGYVASGEEVTAGKPDFPEIFTVCKDLPVSDQRVKAGWPCHGPVPWPNNTYQKSMKAFMGELGLAGERLLKLTALGFELPINTFTDLTRNGWHHMRVLRFPPQTSTMSSGIGAHTDYGLLVIAAQDDVGGLYIRPPVEGEKRNRNWLPGESSAGMFEHDDPWTYVTPVQNVWTVFPGDILQFMTCGQLLSTPHKVRLNTRERFACAYFHEPNFEACAYQVFEPSGNERIHYGEHFTSMFMRCYPDRITTKRIHKDNRLAHFK

Source

organism	Pseudomonas savastanoi
ncbi_taxonomy_id	29438
host_organism	Escherichia coli

Entity 2 non-polymer

description	MANGANESE (II) ION
formula_weight	54.9 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	2-OXOGLUTARIC ACID
formula_weight	146.1 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	282

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6. Citations (1)

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length_a	56.063 Å
length_b	56.063 Å
length_c	100.988 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 43
int_tables_number	78
crystal_system	tetragonal

resolution	1.650 Å
resolution_low	39.640 Å
r_factor	0.1729
r_work	0.1715
r_free	0.1977

fit	/app/data/saxs_computation/sc/9scf/9scf.fit
pddf	/app/data/pr_computation/sc/9scf/9scf.pr.out
profile	/app/data/saxs_computation/sc/9scf/9scf.dat

Fe(II)-2-oxoglutarate-dependent Pseudomonas savastanoi pv phaseolicola 1449B in complex with 2-oxoglutarate

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