1wxr

Crystal structure of Heme Binding protein, an autotransporter hemoglobine protease from pathogenic Escherichia coli

Method: X-RAY DIFFRACTION D_max: 139.0 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

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1wxr
沉积日期 deposition_date	2005-01-31
结构标题 title	Crystal structure of Heme Binding protein, an autotransporter hemoglobine protease from pathogenic Escherichia coli
关键词 keywords	hemoglobine protease, autotransporter, beta helix, heme uptake, SPATE, HYDROLASE; HYDROLASE
实验方法 method	X-RAY DIFFRACTION

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

回转半径 Rg (Guinier) rg_guinier	40.33 Å
回转半径 Rg (电子) rg_electron	40.61 Å
零角强度 I(0) i0	199505000.00
分子量 molecular_weight	110560.0 kDa
排除体积 excluded_volume	136510 Å³
包络体积 envelope_volume	180290 Å³
水化壳体积 shell_volume	40158 Å³
包络直径 envelope_diameter	144.6 Å
壳层 Rg shell_rg	42.08 Å
包络 Rg envelope_rg	40.67 Å
形状 Rg shape_rg	40.60 Å
总 Rg total_rg	40.75 Å
总原子数 total_atoms	7802
残基数 n_residues	1035
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

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

最大尺寸 Dmax dmax	139.0 Å
Rg (实空间) rg_real	40.62 Å
Rg 误差 (实空间) rg_real_error	1.24 Å
I(0) (实空间) i0_real	1.9950e+08
I(0) 误差 (实空间) i0_real_error	3.1770e+06
Rg (倒空间) rg_reciprocal	40.33 Å
I(0) (倒空间) i0_reciprocal	199400000.0000
解质量估计 total_estimate	0.8220
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	42.8 Å
偏度 Skewness skewness	0.494
峰度 Kurtosis kurtosis	-0.391
角度范围 angular_range	— – 0.1950 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	16300000.0000
实空间数据点数 n_real_points	40
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.787; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.673; Smooth: 0.646

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

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5. 实体与聚合体信息 (2)

Entity 1 polymer

描述 description	haemoglobin protease
分子量 formula_weight	111963.6 kDa
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	8197

GTVNNELGYQLFRDFAENKGMFRPGATNIAIYNKQGEFVGTLDKAAMPDFSAVDSEIGVATLINPQYIASVKHNGGYTNVSFGDGENRYNIVDRNNAPSLDFHAPRLDKLVTEVAPTAVTAQGAVAGAYLDKERYPVFYRLGSGTQYIKDSNGQLTKMGGAYSWLTGGTVGSLSSYQNGEMISTSSGLVFDYKLNGAMPIYGEAGDSGSPLFAFDTVQNKWVLVGVLTAGNGAGGRGNNWAVIPLDFIGQKFNEDNDAPVTFRTSEGGALEWSFNSSTGAGALTQGTTTYAMHGQQGNDLNAGKNLIFQGQNGQINLKDSVSQGAGSLTFRDNYTVTTSNGSTWTGAGIVVDNGVSVNWQVNGVKGDNLHKIGEGTLTVQGTGINEGGLKVGDGKVVLNQQADNKGQVQAFSSVNIASGRPTVVLTDERQVNPDTVSWGYRGGTLDVNGNSLTFHQLKAADYGAVLANNVDKRATITLDYALRADKVALNGWSESGKGTAGNLYKYNNPYTNTTDYFILKQSTYGYFPTDQSSNATWEFVGHSQGDAQKLVADRFNTAGYLFHGQLKGNLNVDNRLPEGVTGALVMDGAADISGTFTQENGRLTLQGHPVIHAYNTQSVADKLAASGDHSVLTQPTSFSQEDWENRSFTFDRLSLKNTDFGLGRNATLNTTIQADNSSVTLGDSRVFIDKNDGQGTAFTLEEGTSVATKDADKSVFNGTVNLDNQSVLNINDIFNGGIQANNSTVNISSDSAVLGNSTLTSTALNLNKGANALASQSFVSDGPVNISDATLSLNSRPDEVSHTLLPVYDYAGSWNLKGDDARLNVGPYSMLSGNINVQDKGTVTLGGEGELSPDLTLQNQMLYSLFNGYRNIWSGSLNAPDATVSMTDTQWSMNGNSTAGNMKLNRTIVGFNGGTSPFTTLTTDNLDAVQSAFVMRTDLNKADKLVINKSATGHDNSIWVNFLKKPSNKDTLDIPLVSAPEATADNLFRASTRVVGFSDVTPILSVRKEDGKKEWVLDGYQVARNDGQGKAAATFMHISYNNFITEVN

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 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	395

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6. 折叠分类 (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

结构域编号 domain_id	1wxrA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	10 — Thrombin, subunit H
同源超家族 H-superfamily homologous superfamily	120 —

结构域编号 domain_id	1wxrA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	160 — 3 Solenoid
拓扑 Topology topology	20 — Pectate Lyase C-like
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1wxrA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	160 — Double Stranded RNA Binding Domain
同源超家族 H-superfamily homologous superfamily	280 —

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7. 引用文献 (1)

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晶胞边长 a length_a	115.028 Å
晶胞边长 b length_b	115.028 Å
晶胞边长 c length_c	437.057 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	120.00 °
晶胞分子数 Z z_pdb	12

空间群 space_group	P 61 2 2
空间群编号 int_tables_number	178
晶系 crystal_system	—

分辨率 resolution	2.200 Å
最低分辨率 resolution_low	29.360 Å
R 因子 r_factor	0.2051
R_work r_work	0.2031
R_free r_free	0.2426

fit	/app/data/saxs_computation/wx/1wxr/1wxr.fit
pddf	/app/data/pr_computation/wx/1wxr/1wxr.pr.out
profile	/app/data/saxs_computation/wx/1wxr/1wxr.dat