2fge

Crystal structure of presequence protease PreP from Arabidopsis thaliana

Method: X-RAY DIFFRACTION D_max: 155.1 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	2fge
沉积日期 deposition_date	2005-12-21
结构标题 title	Crystal structure of presequence protease PreP from Arabidopsis thaliana
关键词 keywords	PEPTIDASOME; PROTEASE-PEPTIDE COMPLEX, HYDROLASE, PLANT PROTEIN; HYDROLASE, PLANT PROTEIN
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	44.75 Å
回转半径 Rg (电子) rg_electron	44.52 Å
零角强度 I(0) i0	740521000.00
分子量 molecular_weight	222970.0 kDa
排除体积 excluded_volume	277550 Å³
包络体积 envelope_volume	366020 Å³
水化壳体积 shell_volume	68989 Å³
包络直径 envelope_diameter	165.0 Å
壳层 Rg shell_rg	48.97 Å
包络 Rg envelope_rg	43.82 Å
形状 Rg shape_rg	44.57 Å
总 Rg total_rg	44.51 Å
总原子数 total_atoms	15552
残基数 n_residues	1930
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	155.1 Å
Rg (实空间) rg_real	44.95 Å
Rg 误差 (实空间) rg_real_error	1.66 Å
I(0) (实空间) i0_real	7.4050e+08
I(0) 误差 (实空间) i0_real_error	1.3470e+07
Rg (倒空间) rg_reciprocal	44.75 Å
I(0) (倒空间) i0_reciprocal	740300000.0000
解质量估计 total_estimate	0.8272
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	44.3 Å
偏度 Skewness skewness	0.449
峰度 Kurtosis kurtosis	-0.461
角度范围 angular_range	— – 0.1750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	241200000.0000
实空间数据点数 n_real_points	36
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.633; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.923; Smooth: 0.928

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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 (6)

Entity 1 polymer

描述 description	zinc metalloprotease (insulinase family)
分子量 formula_weight	112536.4 kDa
突变 mutation	E80Q
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	16500

VATQPAPLYPDVGQDEAEKLGFEKVSEEFISECKSKAILFKHKKTGCEVMSVSNEDENKVFGVVFRTPPKDSTGIPHILQHSVLCGSRKYPVKEPFVELLKGSLHTFLNAFTYPDRTCYPVASTNTKDFYNLVDVYLDAVFFPKCVDDAHTFQQEGWHYELNDPSEDISYKGVVFNEMKGVYSQPDNILGRIAQQALSPENTYGVDSGGDPKDIPNLTFEEFKEFHRQYYHPSNARIWFYGDDDPVHRLRVLSEYLDMFEASPSPNSSKIKFQKLFSEPVRLVEKYPAGRDGDLKKKHMLCVNWLLSEKPLDLQTQLALGFLDHLMLGTPASPLRKILLESGLGEALVSSGLSDELLQPQFGIGLKGVSEENVQKVEELIMDTLKKLAEEGFDNDAVEASMNTIEFSLRENNTGSFPRGLSLMLQSISKWIYDMDPFEPLKYTEPLKALKTRIAEEGSKAVFSPLIEKLILNNSHRVTIEMQPDPEKATQEEVEEKNILEKVKAAMTEEDLAELARATEELKLKQETPDPPEALRCVPSLNLGDIPKEPTYVPTEVGDINGVKVLRHDLFTNDIIYTEVVFDIGSLKHELLPLVPLFCQSLLEMGTKDLTFVQLNQLIGRKTGGISVYPLTSSVRGKDEPCSKIIVRGKSMAGRADDLFNLMNCLLQEVQFTDQQRFKQFVSQSRARMENRLRGSGHGIAAARMDAMLNIAGWMSEQMGGLSYLEFLHTLEKKVDEDWEGISSSLEEIRRSLLARNGCIVNMTADGKSLTNVEKSVAKFLDLLPENPSGGLVTWDGRLPLRNEAIVIPTQVNYVGKAGNIYSTGYELDGSAYVISKHISNTWLWDRVRVSGGAYGGFCDFDSHSGVFSYLSYRDPNLLKTLDIYDGTGDFLRGLDVDQETLTKAIIGTIGDVDSYQLPDAKGYSSLLRHLLGVTDEERQRKREEILTTSLKDFKDFAQAIDVVRDKGVAVAVASAEDIDAANNERSNFFEVKKAL

来源 Source

来源生物 organism	Arabidopsis thaliana
通用名 common_name	thale cress
NCBI 分类编号 ncbi_taxonomy_id	3702
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

描述 description	nonspecific peptide AALTRA
分子量 formula_weight	602.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

聚合体 Polymer

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

AALTRA

Entity 3 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	2

Entity 4 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 6 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	948

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d2fgea1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.185 — LuxS/MPP-like metallohydrolase
超家族 Superfamily superfamily	d.185.1 — LuxS/MPP-like metallohydrolase
家族 Family family	d.185.1.1 — MPP-like

结构域编号 domain_id	d2fgea2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.185 — LuxS/MPP-like metallohydrolase
超家族 Superfamily superfamily	d.185.1 — LuxS/MPP-like metallohydrolase
家族 Family family	d.185.1.1 — MPP-like

结构域编号 domain_id	d2fgea3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.185 — LuxS/MPP-like metallohydrolase
超家族 Superfamily superfamily	d.185.1 — LuxS/MPP-like metallohydrolase
家族 Family family	d.185.1.1 — MPP-like

结构域编号 domain_id	d2fgea4
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.185 — LuxS/MPP-like metallohydrolase
超家族 Superfamily superfamily	d.185.1 — LuxS/MPP-like metallohydrolase
家族 Family family	d.185.1.1 — MPP-like

结构域编号 domain_id	d2fgeb1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.185 — LuxS/MPP-like metallohydrolase
超家族 Superfamily superfamily	d.185.1 — LuxS/MPP-like metallohydrolase
家族 Family family	d.185.1.1 — MPP-like

结构域编号 domain_id	d2fgeb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.185 — LuxS/MPP-like metallohydrolase
超家族 Superfamily superfamily	d.185.1 — LuxS/MPP-like metallohydrolase
家族 Family family	d.185.1.1 — MPP-like

结构域编号 domain_id	d2fgeb3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.185 — LuxS/MPP-like metallohydrolase
超家族 Superfamily superfamily	d.185.1 — LuxS/MPP-like metallohydrolase
家族 Family family	d.185.1.1 — MPP-like

结构域编号 domain_id	d2fgeb4
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.185 — LuxS/MPP-like metallohydrolase
超家族 Superfamily superfamily	d.185.1 — LuxS/MPP-like metallohydrolase
家族 Family family	d.185.1.1 — MPP-like

CATH v4.4 (8 domains)

结构域编号 domain_id	2fgeA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	830 — Cytochrome Bc1 Complex; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Metalloenzyme, LuxS/M16 peptidase-like

结构域编号 domain_id	2fgeA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	830 — Cytochrome Bc1 Complex; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Metalloenzyme, LuxS/M16 peptidase-like

结构域编号 domain_id	2fgeA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	830 — Cytochrome Bc1 Complex; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Metalloenzyme, LuxS/M16 peptidase-like

结构域编号 domain_id	2fgeA04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	830 — Cytochrome Bc1 Complex; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Metalloenzyme, LuxS/M16 peptidase-like

结构域编号 domain_id	2fgeB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	830 — Cytochrome Bc1 Complex; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Metalloenzyme, LuxS/M16 peptidase-like

结构域编号 domain_id	2fgeB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	830 — Cytochrome Bc1 Complex; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Metalloenzyme, LuxS/M16 peptidase-like

结构域编号 domain_id	2fgeB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	830 — Cytochrome Bc1 Complex; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Metalloenzyme, LuxS/M16 peptidase-like

结构域编号 domain_id	2fgeB04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	830 — Cytochrome Bc1 Complex; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Metalloenzyme, LuxS/M16 peptidase-like

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7. 引用文献 (2)

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晶胞边长 a length_a	110.834 Å
晶胞边长 b length_b	114.332 Å
晶胞边长 c length_c	162.984 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	8

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	2.100 Å
最低分辨率 resolution_low	93.660 Å
R 因子 r_factor	0.2090
R_work r_work	0.2060
R_free r_free	0.2560

fit	/app/data/saxs_computation/fg/2fge/2fge.fit
pddf	/app/data/pr_computation/fg/2fge/2fge.pr.out
profile	/app/data/saxs_computation/fg/2fge/2fge.dat

Crystal structure of presequence protease PreP from Arabidopsis thaliana

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

精修参数 Refinement

衍射实验 Diffraction

5. 实体与聚合体信息 (6)

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 non-polymer

Entity 6 water

6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)