SAXSdb — 1w9v

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1w9v
沉积日期 deposition_date	2004-10-19
结构标题 title	Specificity and affinity of natural product cyclopentapeptide argifin against Aspergillus fumigatus
关键词 keywords	CHITINASE, ARGIFIN, CHITINASE INHIBITORS, CYCLOPENTAPEPTIDE INHIBITORS, 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	36.54 Å
回转半径 Rg (电子) rg_electron	36.69 Å
零角强度 I(0) i0	125702000.00
分子量 molecular_weight	88745.0 kDa
排除体积 excluded_volume	110010 Å³
包络体积 envelope_volume	133620 Å³
水化壳体积 shell_volume	32314 Å³
包络直径 envelope_diameter	126.4 Å
壳层 Rg shell_rg	39.80 Å
包络 Rg envelope_rg	36.50 Å
形状 Rg shape_rg	36.68 Å
总 Rg total_rg	36.93 Å
总原子数 total_atoms	6267
残基数 n_residues	790
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	123.9 Å
Rg (实空间) rg_real	36.93 Å
Rg 误差 (实空间) rg_real_error	1.71 Å
I(0) (实空间) i0_real	1.2570e+08
I(0) 误差 (实空间) i0_real_error	2.4570e+06
Rg (倒空间) rg_reciprocal	36.69 Å
I(0) (倒空间) i0_reciprocal	125700000.0000
解质量估计 total_estimate	0.7589
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	28.8 Å
偏度 Skewness skewness	0.462
峰度 Kurtosis kurtosis	-0.694
角度范围 angular_range	— – 0.2150 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	21430000.0000
实空间数据点数 n_real_points	44
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.546; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.460; Smooth: 0.771

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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 (4)

Entity 1 polymer

描述 description	CHITINASE
分子量 formula_weight	47661.8 kDa
EC 编号 ec_number	3.2.1.14
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	7347

MRFATSTIVKVALLLSSLCVDAAVMWNRDTSSTDLEARASSGYRSVVYFVNWAIYGRNHNPQDLPVERLTHVLYAFANVRPETGEVYMTDSWADIEKHYPGDSWSDTGNNVYGCIKQLYLLKKQNRNLKVLLSIGGWTYSPNFAPAASTDAGRKNFAKTAVKLLQDLGFDGLDIDWEYPENDQQANDFVLLLKEVRTALDSYSAANAGGQHFLLTVASPAGPDKIKVLHLKDMDQQLDFWNLMAYDYAGSFSSLSGHQANVYNDTSNPLSTPFNTQTALDLYRAGGVPANKIVLGMPLYGRSFANTDGPGKPYNGVGQGSWENGVWDYKALPQAGATEHVLPDIMASYSYDATNKFLISYDNPQVANLKSGYIKSLGLGGAMWWDSSSDKTGSDSLITTVVNALGGTGVFEQSQNELDYPVSQYDNLRNGMQT

来源 Source

来源生物 organism	ASPERGILLUS FUMIGATUS
NCBI 分类编号 ncbi_taxonomy_id	746128
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 polymer

描述 description	ARGIFIN
分子量 formula_weight	693.7 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	C,D

XFDDA

Entity 3 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

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	1080

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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	d1w9va1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.8 — (Trans)glycosidases
家族 Family family	c.1.8.5 — Type II chitinase

结构域编号 domain_id	d1w9va2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.26 — FKBP-like
超家族 Superfamily superfamily	d.26.3 — Chitinase insertion domain
家族 Family family	d.26.3.1 — Chitinase insertion domain

结构域编号 domain_id	d1w9vb1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.8 — (Trans)glycosidases
家族 Family family	c.1.8.5 — Type II chitinase

结构域编号 domain_id	d1w9vb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.26 — FKBP-like
超家族 Superfamily superfamily	d.26.3 — Chitinase insertion domain
家族 Family family	d.26.3.1 — Chitinase insertion domain

CATH v4.4 (4 domains)

结构域编号 domain_id	1w9vA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	80 — Glycosidases

结构域编号 domain_id	1w9vA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	50 — Chitinase A; domain 3
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1w9vB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	80 — Glycosidases

结构域编号 domain_id	1w9vB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	10 — Roll
拓扑 Topology topology	50 — Chitinase A; domain 3
同源超家族 H-superfamily homologous superfamily	10 —

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7. 引用文献 (1)

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晶胞边长 a length_a	117.704 Å
晶胞边长 b length_b	117.704 Å
晶胞边长 c length_c	99.783 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 41
空间群编号 int_tables_number	76
晶系 crystal_system	—

分辨率 resolution	2.000 Å
最低分辨率 resolution_low	19.820 Å
R 因子 r_factor	0.2240
R_work r_work	0.2240
R_free r_free	0.2480

fit	/app/data/saxs_computation/w9/1w9v/1w9v.fit
pddf	/app/data/pr_computation/w9/1w9v/1w9v.pr.out
profile	/app/data/saxs_computation/w9/1w9v/1w9v.dat

Specificity and affinity of natural product cyclopentapeptide argifin against Aspergillus fumigatus

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 (4)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

Entity 3 non-polymer

Entity 4 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)