SAXSdb — 1m9s

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1m9s
沉积日期 deposition_date	2002-07-29
结构标题 title	Crystal structure of Internalin B (InlB), a Listeria monocytogenes virulence protein containing SH3-like domains.
关键词 keywords	internalin, cell invasion, GW domains, SH3 domains, SIGNALING PROTEIN; SIGNALING 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	63.41 Å
回转半径 Rg (电子) rg_electron	65.32 Å
零角强度 I(0) i0	52550800.00
分子量 molecular_weight	60312.0 kDa
排除体积 excluded_volume	75118 Å³
包络体积 envelope_volume	136430 Å³
水化壳体积 shell_volume	18448 Å³
包络直径 envelope_diameter	196.8 Å
壳层 Rg shell_rg	62.38 Å
包络 Rg envelope_rg	60.89 Å
形状 Rg shape_rg	65.36 Å
总 Rg total_rg	65.09 Å
总原子数 total_atoms	4182
残基数 n_residues	523
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	213.4 Å
Rg (实空间) rg_real	64.88 Å
Rg 误差 (实空间) rg_real_error	3.08 Å
I(0) (实空间) i0_real	5.2550e+07
I(0) 误差 (实空间) i0_real_error	1.1820e+06
Rg (倒空间) rg_reciprocal	61.97 Å
I(0) (倒空间) i0_reciprocal	52280000.0000
解质量估计 total_estimate	0.5452
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	25.6 Å
偏度 Skewness skewness	0.275
峰度 Kurtosis kurtosis	-1.327
角度范围 angular_range	— – 0.1250 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	1493000.0000
实空间数据点数 n_real_points	26
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.001; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.003; Smooth: 0.084

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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	Internalin B
分子量 formula_weight	68622.1 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	4247

MGETITVSTPIKQIFPDDAFAETIKDNLKKKSVTDAVTQNELNSIDQIIANNSDIKSVQGIQYLPNVTKLFLNGNKLTDIKPLTNLKNLGWLFLDENKIKDLSSLKDLKKLKSLSLEHNGISDINGLVHLPQLESLYLGNNKITDITVLSRLTKLDTLSLEDNQISDIVPLAGLTKLQNLYLSKNHISDLRALAGLKNLDVLELFSQECLNKPINHQSNLVVPNTVKNTDGSLVTPEIISDDGDYEKPNVKWHLPEFTNEVSFIFYQPVTIGKAKARFHGRVTQPLKEVYTVSYDVDGTVIKTKVEAGTRITAPKPPTKQGYVFKGWYTEKNGGHEWNFNTDYMSGNDFTLYAVFKAETTEKTVNLTRYVKYIRGNAGIYKLPREDNSLKQGTLASHRCKALTVDREARNGGKLWYRLKNIGWTKAENLSLDRYDKMEYDKGVTAYARVRNASGNSVWTKPYNTAGAKHVNKLSVYQGKNMRILREAKTPITTWYQFSIGGKVIGWVDTRALNTFYKQSMEKPTRLTRYVSANKAGESYYKVPVADNPVKRGTLAKYKNQKLIVDCQATIEGQLWYRIRTSSTFIGWTKAANLRAQKLEHHHHHH

来源 Source

来源生物 organism	Listeria monocytogenes
NCBI 分类编号 ncbi_taxonomy_id	1639
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	TERBIUM(III) ION
分子量 formula_weight	158.9 kDa
来源方法 src_method	syn
拷贝数 entity_count	7

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	1

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	65

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6. 折叠分类 (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

结构域编号 domain_id	d1m9sa1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.18 — E set domains
家族 Family family	b.1.18.15 — Internalin Ig-like domain

结构域编号 domain_id	d1m9sa2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.34 — SH3-like barrel
超家族 Superfamily superfamily	b.34.11 — Prokaryotic SH3-related domain
家族 Family family	b.34.11.1 — GW domain

结构域编号 domain_id	d1m9sa3
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.34 — SH3-like barrel
超家族 Superfamily superfamily	b.34.11 — Prokaryotic SH3-related domain
家族 Family family	b.34.11.1 — GW domain

结构域编号 domain_id	d1m9sa4
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.34 — SH3-like barrel
超家族 Superfamily superfamily	b.34.11 — Prokaryotic SH3-related domain
家族 Family family	b.34.11.1 — GW domain

结构域编号 domain_id	d1m9sa5
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
超家族 Superfamily superfamily	c.10.2 — L domain-like
家族 Family family	c.10.2.1 — Internalin LRR domain

CATH v4.4 (5 domains)

结构域编号 domain_id	1m9sA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	80 — Alpha-Beta Horseshoe
拓扑 Topology topology	10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
同源超家族 H-superfamily homologous superfamily	10 — Ribonuclease Inhibitor

结构域编号 domain_id	1m9sA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	1220 —

结构域编号 domain_id	1m9sA03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	170 —

结构域编号 domain_id	1m9sA04
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	170 —

结构域编号 domain_id	1m9sA05
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	170 —

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7. 引用文献 (1)

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晶胞边长 a length_a	48.500 Å
晶胞边长 b length_b	330.900 Å
晶胞边长 c length_c	182.400 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	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	2.650 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.2740
R_work r_work	0.2730
R_free r_free	0.3020

fit	/app/data/saxs_computation/m9/1m9s/1m9s.fit
pddf	/app/data/pr_computation/m9/1m9s/1m9s.pr.out
profile	/app/data/saxs_computation/m9/1m9s/1m9s.dat

Crystal structure of Internalin B (InlB), a Listeria monocytogenes virulence protein containing SH3-like domains.

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution