1zvr

Crystal Structure of MTMR2 in complex with phosphatidylinositol 3,5-bisphosphate

Method: X-RAY DIFFRACTION D_max: 88.3 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	1zvr
沉积日期 deposition_date	2005-06-02
结构标题 title	Crystal Structure of MTMR2 in complex with phosphatidylinositol 3,5-bisphosphate
关键词 keywords	Protein-Phosphoinositide Complex, 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	25.32 Å
回转半径 Rg (电子) rg_electron	24.22 Å
零角强度 I(0) i0	59081600.00
分子量 molecular_weight	60259.0 kDa
排除体积 excluded_volume	75470 Å³
包络体积 envelope_volume	87259 Å³
水化壳体积 shell_volume	29779 Å³
包络直径 envelope_diameter	89.8 Å
壳层 Rg shell_rg	31.91 Å
包络 Rg envelope_rg	24.73 Å
形状 Rg shape_rg	24.18 Å
总 Rg total_rg	25.15 Å
总原子数 total_atoms	4248
残基数 n_residues	514
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	88.3 Å
Rg (实空间) rg_real	25.34 Å
Rg 误差 (实空间) rg_real_error	0.55 Å
I(0) (实空间) i0_real	5.9080e+07
I(0) 误差 (实空间) i0_real_error	7.9590e+05
Rg (倒空间) rg_reciprocal	25.34 Å
I(0) (倒空间) i0_reciprocal	59080000.0000
解质量估计 total_estimate	0.8542
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	29.4 Å
偏度 Skewness skewness	0.448
峰度 Kurtosis kurtosis	-0.096
角度范围 angular_range	— – 0.3150 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	11460000.0000
实空间数据点数 n_real_points	64
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.721; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.946; Smooth: 0.992

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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	Myotubularin-related protein 2
分子量 formula_weight	61104.4 kDa
EC 编号 ec_number	3.1.3.-
突变 mutation	C417S
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	4646

MASMEEPPLLPGENIKDMAKDVTYICPFTGAVRGTLTVTNYRLYFKSMERDPPFVLDASLGVINRVEKIGGASSRGENSYGLETVCKDIRNLRFAHKPEGRTRRSIFENLMKYAFPVSNNLPLFAFEYKEVFPENGWKLYDPLLEYRRQGIPNESWRITKINERYELCDTYPALLVVPANIPDEELKRVASFRSRGRIPVLSWIHPESQATITRCSQPMVGVSGKRSKEDEKYLQAIMDSNAQSHKIFIFDARPSVNAVANKAKGGGYESEDAYQNAELVFLDIHNIHVMRESLRKLKEIVYPNIEETHWLSNLESTHWLEHIKLILAGALRIADKVESGKTSVVVHSSDGWDRTAQLTSLAMLMLDGYYRTIRGFEVLVEKEWLSFGHRFQLRVGHGDKNHADADRSPVFLQFIDCVWQMTRQFPTAFEFNEYFLITILDHLYSCLFGTFLCNSEQQRGKENLPKRTVSLWSYINSQLEDFTNPLYGSYSNHVLYPVASMRHLELWVGYYIRWNPRAAALEHHHHHH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	1,2-ETHANEDIOL
分子量 formula_weight	62.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 3 non-polymer

描述 description	;(1S)-2-(1-HYDROXYBUTOXY)-1-{[(HYDROXY{[(2R,3S,5R,6S)-2,4,6-TRIHYDROXY-3,5-BIS(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL)OXY]METHYL}ETHYL BUTYRATE ;
分子量 formula_weight	636.4 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	398

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6. 折叠分类 (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1zvra1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.55 — PH domain-like barrel
超家族 Superfamily superfamily	b.55.1 — PH domain-like
家族 Family family	b.55.1.8 — GRAM domain

结构域编号 domain_id	d1zvra2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.45 — (Phosphotyrosine protein) phosphatases II
超家族 Superfamily superfamily	c.45.1 — (Phosphotyrosine protein) phosphatases II
家族 Family family	c.45.1.3 — Myotubularin-like phosphatases

CATH v4.4 (1 domains)

结构域编号 domain_id	1zvrA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	29 — PH-domain like
同源超家族 H-superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

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7. 引用文献 (1)

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晶胞边长 a length_a	66.180 Å
晶胞边长 b length_b	66.180 Å
晶胞边长 c length_c	262.370 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 21 2
空间群编号 int_tables_number	92
晶系 crystal_system	—

分辨率 resolution	1.980 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	—
R_work r_work	0.2280
R_free r_free	0.2520

fit	/app/data/saxs_computation/zv/1zvr/1zvr.fit
pddf	/app/data/pr_computation/zv/1zvr/1zvr.pr.out
profile	/app/data/saxs_computation/zv/1zvr/1zvr.dat