9lyi

Cryo-EM structure of collagenase H (E416Q mutant) from Hathewaya histolytica in complex with collagen model peptide (Pro-Hyp-Gly)12

Method: ELECTRON MICROSCOPY D_max: 94.8 Å Quality: EXCELLENT

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9lyi
沉积日期 deposition_date	2025-02-20
结构标题 title	Cryo-EM structure of collagenase H (E416Q mutant) from Hathewaya histolytica in complex with collagen model peptide (Pro-Hyp-Gly)12
关键词 keywords	Collagenase, Hathewaya histolytica, Clostridium histolyticum, METAL BINDING PROTEIN; METAL BINDING PROTEIN
实验方法 method	ELECTRON MICROSCOPY

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	30.12 Å
回转半径 Rg (电子) rg_electron	29.32 Å
零角强度 I(0) i0	130821000.00
分子量 molecular_weight	90726.0 kDa
排除体积 excluded_volume	113440 Å³
包络体积 envelope_volume	139120 Å³
水化壳体积 shell_volume	39284 Å³
包络直径 envelope_diameter	94.5 Å
壳层 Rg shell_rg	36.98 Å
包络 Rg envelope_rg	28.93 Å
形状 Rg shape_rg	29.30 Å
总 Rg total_rg	30.09 Å
总原子数 total_atoms	6404
残基数 n_residues	786
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	94.8 Å
Rg (实空间) rg_real	30.02 Å
Rg 误差 (实空间) rg_real_error	0.55 Å
I(0) (实空间) i0_real	1.3080e+08
I(0) 误差 (实空间) i0_real_error	1.8700e+06
Rg (倒空间) rg_reciprocal	30.06 Å
I(0) (倒空间) i0_reciprocal	130800000.0000
解质量估计 total_estimate	0.9069
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	37.6 Å
偏度 Skewness skewness	0.217
峰度 Kurtosis kurtosis	-0.492
角度范围 angular_range	— – 0.2650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	21110000.0000
实空间数据点数 n_real_points	54
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.937; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.976

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (5)

Entity 1 polymer

描述 description	Collagenase ColH
分子量 formula_weight	112305.2 kDa
EC 编号 ec_number	3.4.24.3
突变 mutation	E416Q
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	6478

GSVQNESKRYTVSYLKTLNYYDLVDLLVKTEIENLPDLFQYSSDAKEFYGNKTRMSFIMDEIGRRAPQYTEIDHKGIPTLVEVVRAGFYLGFHNKELNEINKRSFKERVIPSILAIQKNPNFKLGTEVQDKIVSATGLLAGNETAPPEVVNNFTPILQDCIKNIDRYALDDLKSKALFNVLAAPTYDITEYLRATKEKPENTPWYGKIDGFINELKKLALYGKINDNNSWIIDNGIYHIAPLGKLHSNNKIGIETLTEVMKVYPYLSMQHLQSADQIKRHYDSKDAEGNKIPLDKFKKEGKEKYCPKTYTFDDGKVIIKAGARVEEEKVKRLYWASKEVNSQFFRVYGIDKPLEEGNPDDILTMVIYNSPEEYKLNSVLYGYDTNNGGMYIEPEGTFFTYEREAQESTYTLEELFRHQYTHYLQGRYAVPGQWGRTKLYDNDRLTWYEEGGAELFAGSTRTSGILPRKSIVSNIHNTTRNNRYKLSDTVHSKYGASFEFYNYACMFMDYMYNKDMGILNKLNDLAKNNDVDGYDNYIRDLSSNYALNDKYQDHMQERIDNYENLTVPFVADDYLVRHAYKNPNEIYSEISEVAKLKDAKSEVKKSQYFSTFTLRGSYTGGASKGKLEDQKAMNKFIDDSLKKLDTYSWSGYKTLTAYFTNYKVDSSNRVTYDVVFHGYLPNEGDSKNSLPYGKINGTYKGTEKEKIKFSSEGSFDPDGKIVSYEWDFGDGNKSNEENPEHSYDKVGTYTVKLKVTDDKGESSVSTTTAEIKDLSENKLPVIYMHVPKSGALNQKVVFYGKGTYDPDGSIAGYQWDFGDGSDFSSEQNPSHVYTKKGEYTVTLRVMDSSGQMSEKTMKIKITDPVYPIGTEKEPNNSKETASGPIVPGIPVSGTIENTSDQDYFYFDVITPGEVKIDINKLGYGGATWVVYDENNNAVSYATDDGQNLSGKFKADKPGRYYIHLYMFNGSYMPYRINIEGSVGR

来源 Source

来源生物 organism	Hathewaya histolytica
NCBI 分类编号 ncbi_taxonomy_id	1498
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	(Pro-Hyp-Gly)12
分子量 formula_weight	3225.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,C,D

PPGPPGPPGPPGPPGPPGPPGPPGPPGPPGPPGPPG

Entity 3 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	74

▶

7. 引用文献 (1)

▶

晶胞边长 a length_a	1.000 Å
晶胞边长 b length_b	1.000 Å
晶胞边长 c length_c	1.000 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	—

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	triclinic

分辨率 resolution	2.80 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	318280

fit	/app/data/saxs_computation/ly/9lyi/9lyi.fit
pddf	/app/data/pr_computation/ly/9lyi/9lyi.pr.out
profile	/app/data/saxs_computation/ly/9lyi/9lyi.dat

Cryo-EM structure of collagenase H (E416Q mutant) from Hathewaya histolytica in complex with collagen model peptide (Pro-Hyp-Gly)12

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

4. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

冷冻电镜 EM 3D

5. 实体与聚合体信息 (5)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)