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9pz4

Crystal structure of 2-methoxyhydroquinone dioxygenase (MhdA) from Gelatoporia subvermispora

Method: X-RAY DIFFRACTION D_max: 117.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9pz4
deposition_date	2025-08-08
last_revision	2026-06-10
title	Crystal structure of 2-methoxyhydroquinone dioxygenase (MhdA) from Gelatoporia subvermispora
keywords	Dioxygenase, Vanillate, 2-methoxyhydroquinone, white-rot fungi, lignin, 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	39.69 Å
rg_electron	38.57 Å
i0	1392500000.00
molecular_weight	311440.0 kDa
excluded_volume	390100 Å³
envelope_volume	464300 Å³
shell_volume	91343 Å³
envelope_diameter	123.4 Å
shell_rg	50.24 Å
envelope_rg	38.38 Å
shape_rg	38.56 Å
total_rg	39.11 Å
total_atoms	21999
n_residues	2784
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	117.3 Å
rg_real	39.26 Å
rg_real_error	0.50 Å
i0_real	1.3930e+09
i0_real_error	2.2790e+07
rg_reciprocal	39.53 Å
i0_reciprocal	1393000000.0000
total_estimate	0.8957
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	55.7 Å
skewness	-0.009
kurtosis	-0.558
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	2192000000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.947; Smooth: 0.945

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	homogentisate 1,2-dioxygenase
formula_weight	55236.0 kDa
ec_number	1.13.11.5
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F
atom_count	23798

MGSSHHHHHHSSGLVPRGSHMASNNATGSSFTATAQGTYATSPTKEDPYKYQTGFGNRFMSEALPGVLPQGQNTPQKLKYDLYPECINGTVFTAPRASNQLAWMYRIQPSASHSGFIETTGYGENIVSNFSLGNPKIHISPPQIHWEPLEIPSGNAQVDFIDSLKTYVGAGDPMSGEGVAIHMYNANASMEKRAFVNVDGDFLFIPQEGRLDIQTELGKLMVKPGEIAVVQRGLKFKINLPDGAARGYLEEIYGVHWELPELGVVGANGLASPRDFQSPVAFFEVDQSAWEVVYKNLGKLFTCKQSHTPFDVVAWHGNYIPYKYDLRKFIHVNSVTRDHMDPSLYTVLTAKSKTPDAPIADFCVASERWDVGEGFRPPFYHRNTAVEALGIIFGDGKREPNAPIAPGGFYYQNSMTPHGPAWEQFKAATEMDLKPMKIFENQMLLIFESARTLVLTDYAAKTSARREFDVSHHEALRPQFLNHIDSIKRELAEAKD

Source

organism	Gelatoporia subvermispora B
common_name	White-rot fungus
ncbi_taxonomy_id	914234
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	FE (III) ION
formula_weight	55.8 kDa
src_method	syn
entity_count	6

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1701

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6. Citations (1)

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length_a	86.650 Å
length_b	176.170 Å
length_c	184.150 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	24

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.250 Å
resolution_low	39.260 Å
r_factor	0.1700
r_work	0.1676
r_free	0.2154

fit	/app/data/saxs_computation/pz/9pz4/9pz4.fit
pddf	/app/data/pr_computation/pz/9pz4/9pz4.pr.out
profile	/app/data/saxs_computation/pz/9pz4/9pz4.dat