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9wdc

;Cryo-EM structure of collagenase H (E416Q mutant) from Hathewaya histolytica bound to C-terminal region of the collagen-binding protein ColH (Pro-Pro-Gly)10 ;

Method: ELECTRON MICROSCOPY D_max: 93.4 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9wdc
deposition_date	2025-08-18
title	;Cryo-EM structure of collagenase H (E416Q mutant) from Hathewaya histolytica bound to C-terminal region of the collagen-binding protein ColH (Pro-Pro-Gly)10 ;
keywords	Collagenase, Hathewaya histolytica, Clostridium histolyticum, METAL BINDING PROTEIN; METAL BINDING PROTEIN
method	ELECTRON MICROSCOPY

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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	29.66 Å
rg_electron	28.87 Å
i0	135031000.00
molecular_weight	92659.0 kDa
excluded_volume	115970 Å³
envelope_volume	138270 Å³
shell_volume	39467 Å³
envelope_diameter	93.1 Å
shell_rg	36.72 Å
envelope_rg	28.66 Å
shape_rg	28.84 Å
total_rg	29.65 Å
total_atoms	6544
n_residues	817
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	93.4 Å
rg_real	29.57 Å
rg_real_error	0.55 Å
i0_real	1.3500e+08
i0_real_error	1.8890e+06
rg_reciprocal	29.61 Å
i0_reciprocal	135000000.0000
total_estimate	0.9042
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	35.2 Å
skewness	0.249
kurtosis	-0.462
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	21640000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.926; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.975

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Collagenase ColH
formula_weight	112305.2 kDa
ec_number	3.4.24.3
mutation	E416Q
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	7067

GSVQNESKRYTVSYLKTLNYYDLVDLLVKTEIENLPDLFQYSSDAKEFYGNKTRMSFIMDEIGRRAPQYTEIDHKGIPTLVEVVRAGFYLGFHNKELNEINKRSFKERVIPSILAIQKNPNFKLGTEVQDKIVSATGLLAGNETAPPEVVNNFTPILQDCIKNIDRYALDDLKSKALFNVLAAPTYDITEYLRATKEKPENTPWYGKIDGFINELKKLALYGKINDNNSWIIDNGIYHIAPLGKLHSNNKIGIETLTEVMKVYPYLSMQHLQSADQIKRHYDSKDAEGNKIPLDKFKKEGKEKYCPKTYTFDDGKVIIKAGARVEEEKVKRLYWASKEVNSQFFRVYGIDKPLEEGNPDDILTMVIYNSPEEYKLNSVLYGYDTNNGGMYIEPEGTFFTYEREAQESTYTLEELFRHQYTHYLQGRYAVPGQWGRTKLYDNDRLTWYEEGGAELFAGSTRTSGILPRKSIVSNIHNTTRNNRYKLSDTVHSKYGASFEFYNYACMFMDYMYNKDMGILNKLNDLAKNNDVDGYDNYIRDLSSNYALNDKYQDHMQERIDNYENLTVPFVADDYLVRHAYKNPNEIYSEISEVAKLKDAKSEVKKSQYFSTFTLRGSYTGGASKGKLEDQKAMNKFIDDSLKKLDTYSWSGYKTLTAYFTNYKVDSSNRVTYDVVFHGYLPNEGDSKNSLPYGKINGTYKGTEKEKIKFSSEGSFDPDGKIVSYEWDFGDGNKSNEENPEHSYDKVGTYTVKLKVTDDKGESSVSTTTAEIKDLSENKLPVIYMHVPKSGALNQKVVFYGKGTYDPDGSIAGYQWDFGDGSDFSSEQNPSHVYTKKGEYTVTLRVMDSSGQMSEKTMKIKITDPVYPIGTEKEPNNSKETASGPIVPGIPVSGTIENTSDQDYFYFDVITPGEVKIDINKLGYGGATWVVYDENNNAVSYATDDGQNLSGKFKADKPGRYYIHLYMFNGSYMPYRINIEGSVGR

Source

organism	Hathewaya histolytica
ncbi_taxonomy_id	1498
host_organism	Escherichia coli

Entity 2 polymer

description	(Pro-Pro-Gly)10
formula_weight	2530.8 kDa
src_method	syn
entity_count	3

Polymer

type	polypeptide(L)
strand_id	B,C,D

PPGPPGPPGPPGPPGPPGPPGPPGPPGPPG

Entity 3 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	523

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	2.22 Å
resolution_method	—
num_particles	569950

fit	/app/data/saxs_computation/wd/9wdc/9wdc.fit
pddf	/app/data/pr_computation/wd/9wdc/9wdc.pr.out
profile	/app/data/saxs_computation/wd/9wdc/9wdc.dat

;Cryo-EM structure of collagenase H (E416Q mutant) from Hathewaya histolytica bound to C-terminal region of the collagen-binding protein ColH (Pro-Pro-Gly)10 ;

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

EM 3D

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)