SAXSdb — 1r64

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1r64
沉积日期 deposition_date	2003-10-14
结构标题 title	The 2.2 A crystal structure of Kex2 protease in complex with Ac-Arg-Glu-Lys-boroArg peptidyl boronic acid inhibitor
关键词 keywords	;KEX2, KEXIN, PROTEASE, PROTEIN CONVERTASE, PROHORMONE PROCESSING, PROPROTEIN CONVERTASE, SUBTILISIN, HYDROLASE-HYDROLASE INHIBITOR COMPLEX ;; HYDROLASE/HYDROLASE INHIBITOR
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	31.57 Å
回转半径 Rg (电子) rg_electron	30.96 Å
零角强度 I(0) i0	192334000.00
分子量 molecular_weight	108500.0 kDa
排除体积 excluded_volume	134450 Å³
包络体积 envelope_volume	157760 Å³
水化壳体积 shell_volume	42039 Å³
包络直径 envelope_diameter	107.6 Å
壳层 Rg shell_rg	38.43 Å
包络 Rg envelope_rg	30.94 Å
形状 Rg shape_rg	30.95 Å
总 Rg total_rg	31.56 Å
总原子数 total_atoms	7628
残基数 n_residues	968
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	101.8 Å
Rg (实空间) rg_real	31.55 Å
Rg 误差 (实空间) rg_real_error	0.77 Å
I(0) (实空间) i0_real	1.9230e+08
I(0) 误差 (实空间) i0_real_error	3.1400e+06
Rg (倒空间) rg_reciprocal	31.56 Å
I(0) (倒空间) i0_reciprocal	192300000.0000
解质量估计 total_estimate	0.8938
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	34.6 Å
偏度 Skewness skewness	0.327
峰度 Kurtosis kurtosis	-0.448
角度范围 angular_range	— – 0.2500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	36310000.0000
实空间数据点数 n_real_points	51
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.906; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.899

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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 (8)

Entity 1 polymer

描述 description	Kexin
分子量 formula_weight	52640.0 kDa
EC 编号 ec_number	3.4.21.61
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	8397

LLPVKEAEDKLSINDPLFERQWHLVNPSFPGSDINVLDLWYNNITGAGVVAAIVDDGLDYENEDLKDNFCAEGSWDFNDNTNLPKPRLSDDYHGTRCAGEIAAKKGNNFCGVGVGYNAKISGIRILSGDITTEDEAASLIYGLDVNDIYSCSWGPADDGRHLQGPSDLVKKALVKGVTEGRDSKGAIYVFASGNGGTRGDNCNYDGYTNSIYSITIGAIDHKDLHPPYSEGCSAVMAVTYSSGSGEYIHSSDINGRCSNSHGGTSAAAPLAAGVYTLLLEANPNLTWRDVQYLSILSAVGLEKNADGDWRDSAMGKKYSHRYGFGKIDAHKLIEMSKTWENVNAQTWFYLPTLYVSQSTNSTEETLESVITISEKSLQDANFKRIEHVTVTVDIDTEIRGTTTVDLISPAGIISNLGVVRPRDVSSEGFKDWTFMSVAHWGENGVGDWKIKVKTTENGHRIDFHSWRLKLFGESIDSSKTE

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI 分类编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Saccharomyces cerevisiae

Entity 2 polymer

描述 description	Ac-Arg-Glu-Lys-boroArg peptide inhibitor
分子量 formula_weight	615.5 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	C,D

XREKR

Entity 3 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	221.2 kDa
来源方法 src_method	man
拷贝数 entity_count	3

Entity 5 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	6

Entity 6 non-polymer

描述 description	POTASSIUM ION
分子量 formula_weight	39.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 7 non-polymer

描述 description	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
分子量 formula_weight	209.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 8 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	769

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1r64a1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.18 — Galactose-binding domain-like
超家族 Superfamily superfamily	b.18.1 — Galactose-binding domain-like
家族 Family family	b.18.1.20 — Proprotein convertase P-domain

结构域编号 domain_id	d1r64a2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.41 — Subtilisin-like
超家族 Superfamily superfamily	c.41.1 — Subtilisin-like
家族 Family family	c.41.1.1 — Subtilases

结构域编号 domain_id	d1r64b1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.18 — Galactose-binding domain-like
超家族 Superfamily superfamily	b.18.1 — Galactose-binding domain-like
家族 Family family	b.18.1.20 — Proprotein convertase P-domain

结构域编号 domain_id	d1r64b2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.41 — Subtilisin-like
超家族 Superfamily superfamily	c.41.1 — Subtilisin-like
家族 Family family	c.41.1.1 — Subtilases

CATH v4.4 (4 domains)

结构域编号 domain_id	1r64A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	200 — Peptidase S8/S53 domain

结构域编号 domain_id	1r64A02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	260 — Galactose-binding domain-like

结构域编号 domain_id	1r64B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	200 — Peptidase S8/S53 domain

结构域编号 domain_id	1r64B02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	260 — Galactose-binding domain-like

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7. 引用文献 (1)

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晶胞边长 a length_a	113.541 Å
晶胞边长 b length_b	113.541 Å
晶胞边长 c length_c	364.971 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	24

空间群 space_group	P 65 2 2
空间群编号 int_tables_number	179
晶系 crystal_system	—

分辨率 resolution	2.200 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.1970
R_work r_work	0.1970
R_free r_free	0.2340

fit	/app/data/saxs_computation/r6/1r64/1r64.fit
pddf	/app/data/pr_computation/r6/1r64/1r64.pr.out
profile	/app/data/saxs_computation/r6/1r64/1r64.dat

The 2.2 A crystal structure of Kex2 protease in complex with Ac-Arg-Glu-Lys-boroArg peptidyl boronic acid inhibitor

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 (8)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

Entity 3 branched

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 water

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)