9d26

A widespread heme dechelatase in healthy and pathogenic human microbiomes.

Method: ELECTRON MICROSCOPY D_max: 109.0 Å Quality: GOOD

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	9d26
沉积日期 deposition_date	2024-08-08
结构标题 title	A widespread heme dechelatase in healthy and pathogenic human microbiomes.
关键词 keywords	Iron, Microbiome, Heme, METAL TRANSPORT; METAL TRANSPORT
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	34.42 Å
回转半径 Rg (电子) rg_electron	33.56 Å
零角强度 I(0) i0	312993000.00
分子量 molecular_weight	140820.0 kDa
排除体积 excluded_volume	175690 Å³
包络体积 envelope_volume	233190 Å³
水化壳体积 shell_volume	56195 Å³
包络直径 envelope_diameter	117.4 Å
壳层 Rg shell_rg	41.55 Å
包络 Rg envelope_rg	33.42 Å
形状 Rg shape_rg	33.55 Å
总 Rg total_rg	34.18 Å
总原子数 total_atoms	9900
残基数 n_residues	1254
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	109.0 Å
Rg (实空间) rg_real	34.28 Å
Rg 误差 (实空间) rg_real_error	0.59 Å
I(0) (实空间) i0_real	3.1300e+08
I(0) 误差 (实空间) i0_real_error	4.5470e+06
Rg (倒空间) rg_reciprocal	34.37 Å
I(0) (倒空间) i0_reciprocal	313000000.0000
解质量估计 total_estimate	0.8856
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	42.6 Å
偏度 Skewness skewness	0.250
峰度 Kurtosis kurtosis	-0.306
角度范围 angular_range	— – 0.2300 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	87770000.0000
实空间数据点数 n_real_points	47
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.888; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.864

▶

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

▶

5. 实体与聚合体信息 (4)

Entity 1 polymer

描述 description	HmuS heme dechelatase
分子量 formula_weight	162423.3 kDa
EC 编号 ec_number	6.6.1.2
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	9995

MKKKSKIILGGCIVVAALIGLSVWNTWFSATKIAFVNFQTIQQGSISKANDNSFIKLSEVSLDNLDRLTSYDMVFINGMGLRIVEEQRQQIQQAADKGIPVYTSMATNPANNICNLDSIQQNLIRGYLSNGGKTNYRNMLNYIRKAIDGKASAVPEVEDPIERPSDMLYHAGISNPDDEQEFLTVADYEKFMQENNLYKEGARKIMITGQMADATDLIKALENAGYNVYPVQSMTRFMSFIEEVQPDAVINMAHGRMGDKMVDYLKARNILLFAPLTINSLVDEWENDPMGMSGGFMSQSIVTPEIDGAIRPFALFAQYEDKEGLRHSYAVPERLKTFVSTIDNYLNLKTKPNFEKKVAIYYYKGPGQNALTAAGMEVVPSLYNLLLRMKQEGYNISGLPANAQELGKMIQAQGAVFNAYAEGAFNDFMQNGHPELITKEQYESWVKESLRPEKYQEVVDAFGEFPGNYMVTPDGKLGIARLQFGNVVLLPQNAAGSGDNSFQVVHGTDMAPPHTYIASYLWMQHGFKADALIHFGTHGSLEFTPRKQVALCSNDWPDRLVGAVPHYYLYSIGNVGEGMMAKRRSYATLQSYLTPPFLESSVRGIYRELMEKIKIYNNSQKANKDQESLAVKTLTVKMGIHRDLGLDSMANKPYTEDEIARVENFAEELATEKITGQLYTMGVPYEPERITSSVYAMATEPIAYSLFALDKQRGKATESAEKHRSVFTQQYLMPARLLVERLMANPSLATDELICHTAGITPQELAKARQIEAERNAPKGMMAMMMAAAAKKDQADNEPSGNGHPASAKMEKGPHGKMPAGMKEAMKKMGANMDPEKAMEMAKSMGASPEALKKMEASMKANKDTSTDASGKPAMAGKTEKPQGMSAMMAAMGKAPKEYSKEEVEFALAVAEVERTIKNVGNYKNALLTSPEEELSSLMNALKGGYTAPTPGGDPIANPNTLPTGRNMYAINAEATPTESAWEKGIALAKQTIDRYKQRHNDSIPRKVSYTLWSSEFIETGGATIAQVLYMLGVEPVRDAFGRVSDLKLIPSTELGRPRIDVVVQTSGQLRDLAASRLFLINRAVEMAAAAKDDKYENQVASSVIEAERVLTEKGLSPKDAREISTFRVFGGANGMYGTGIQEMVESGDRWENESEIADTYLNNMGAYYGSEKNWEVFQKFAFEAALTRTDVVVQPRQSNTWGALSLDHVYEFMGGMNLAVRNVTGKDPDAYLSDYRNRNHMKMQELKEAVGVESRTTILNPTYIKEKMKGGASSASEFAEVITNTYGWNVMKPAAIDKELWDNIYNVYVKDELNLGVKQYFEQQNPAALEEMTAVMLESARKGLWQASEEQVAELSKLHTEIVNTYRPSCSGFVCDNAKLRDFIASKADAQTATQYKENISKIREAKASGSNKGVVMKKEEMNQTAENQTNTLSNVAVGIAVIIVILALILFVRKRRKSSQM

来源 Source

来源生物 organism	Bacteroides
NCBI 分类编号 ncbi_taxonomy_id	816
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	PROTOPORPHYRIN IX CONTAINING FE
分子量 formula_weight	616.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	SODIUM ION
分子量 formula_weight	23.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 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	95

▶

7. 引用文献 (2)

▶

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	2.60 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	2133842

fit	/app/data/saxs_computation/d2/9d26/9d26.fit
pddf	/app/data/pr_computation/d2/9d26/9d26.pr.out
profile	/app/data/saxs_computation/d2/9d26/9d26.dat