SAXSdb — 2iw5

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2iw5
沉积日期 deposition_date	2006-06-26
结构标题 title	Structural Basis for CoREST-Dependent Demethylation of Nucleosomes by the Human LSD1 Histone Demethylase
关键词 keywords	;OXIDOREDUCTASE-TRANSCRIPTION REGULATOR COMPLEX, OXIDOREDUCTASE-REPRESSOR COMPLEX, HISTONE DEMETHYLASE, FAD, LSD1, COREST, REPRESSOR, TRANSCRIPTION REGULATION, HOST-VIRUS INTERACTION, CHROMATIN DEMETHYLATION, NUCLEAR PROTEIN, PHOSPHORYLATION, CHROMATIN REGULATOR, NUCLEOSOMES, TRANSCRIPTION, OXIDOREDUCTASE ;; OXIDOREDUCTASE/TRANSCRIPTION REGULATOR
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	43.20 Å
回转半径 Rg (电子) rg_electron	44.58 Å
零角强度 I(0) i0	123845000.00
分子量 molecular_weight	90398.0 kDa
排除体积 excluded_volume	113500 Å³
包络体积 envelope_volume	166110 Å³
水化壳体积 shell_volume	35968 Å³
包络直径 envelope_diameter	158.0 Å
壳层 Rg shell_rg	40.92 Å
包络 Rg envelope_rg	46.07 Å
形状 Rg shape_rg	44.59 Å
总 Rg total_rg	44.34 Å
总原子数 total_atoms	6362
残基数 n_residues	799
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	143.7 Å
Rg (实空间) rg_real	44.24 Å
Rg 误差 (实空间) rg_real_error	1.88 Å
I(0) (实空间) i0_real	1.2380e+08
I(0) 误差 (实空间) i0_real_error	2.2450e+06
Rg (倒空间) rg_reciprocal	43.21 Å
I(0) (倒空间) i0_reciprocal	123700000.0000
解质量估计 total_estimate	0.6318
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	31.1 Å
偏度 Skewness skewness	0.731
峰度 Kurtosis kurtosis	-0.483
角度范围 angular_range	— – 0.1850 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	9298000.0000
实空间数据点数 n_real_points	38
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.319; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.248; Smooth: 0.003

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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 (7)

Entity 1 polymer

描述 description	LYSINE-SPECIFIC HISTONE DEMETHYLASE 1
分子量 formula_weight	74126.8 kDa
EC 编号 ec_number	1.-.-.-
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	6440

PSGVEGAAFQSRLPHDRMTSQEAACFPDIISGPQQTQKVFLFIRNRTLQLWLDNPKIQLTFEATLQQLEAPYNSDTVLVHRVHSYLERHGLINFGIYKRIKPLPTKKTGKVIIIGSGVSGLAAARQLQSFGMDVTLLEARDRVGGRVATFRKGNYVADLGAMVVTGLGGNPMAVVSKQVNMELAKIKQKCPLYEANGQAVPKEKDEMVEQEFNRLLEATSYLSHQLDFNVLNNKPVSLGQALEVVIQLQEKHVKDEQIEHWKKIVKTQEELKELLNKMVNLKEKIKELHQQYKEASEVKPPRDITAEFLVKSKHRDLTALCKEYDELAETQGKLEEKLQELEANPPSDVYLSSRDRQILDWHFANLEFANATPLSTLSLKHWDQDDDFEFTGSHLTVRNGYSCVPVALAEGLDIKLNTAVRQVRYTASGCEVIAVNTRSTSQTFIYKCDAVLCTLPLGVLKQQPPAVQFVPPLPEWKTSAVQRMGFGNLNKVVLCFDRVFWDPSVNLFGHVGSTTASRGELFLFWNLYKAPILLALVAGEAAGIMENISDDVIVGRCLAILKGIFGSSAVPQPKETVVSRWRADPWARGSYSYVAAGSSGNDYDLMAQPITPGPSIPGAPQPIPRLFFAGEHTIRNYPATVHGALLSGLREAGRIADQFLGAMYTL

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

Entity 2 polymer

描述 description	REST COREPRESSOR 1
分子量 formula_weight	26425.7 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	B

MGSSHHHHHHSSGLVPRGSHMASMTGGQQMGRGSEFGRPTETVPQVKKEKHSTQAKNRAKRKPPKGMFLSQEDVEAVSANATAATTVLRQLDMELVSVKRQIQNIKQTNSALKEKLDGGIEPYRLPEVIQKCNARWTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQVKNFFVNYRRRFNIDEVLQEWEAEHGKEETNGPSNQKPVKSPDNSIKMPEEEDEAPVLDVRYASAS

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

Entity 3 non-polymer

描述 description	FLAVIN-ADENINE DINUCLEOTIDE
分子量 formula_weight	785.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	3

Entity 5 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 6 non-polymer

描述 description	AMMONIUM ION
分子量 formula_weight	18.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 7 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	78

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (5 domains)

结构域编号 domain_id	d2iw5a1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
超家族 Superfamily superfamily	a.4.1 — Homeodomain-like
家族 Family family	a.4.1.18 — SWIRM domain

结构域编号 domain_id	d2iw5a2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.3 — FAD/NAD(P)-binding domain
超家族 Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
家族 Family family	c.3.1.2 — FAD-linked reductases, N-terminal domain

结构域编号 domain_id	d2iw5a3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.16 — FAD-linked reductases, C-terminal domain
超家族 Superfamily superfamily	d.16.1 — FAD-linked reductases, C-terminal domain
家族 Family family	d.16.1.5 — L-aminoacid/polyamine oxidase

结构域编号 domain_id	d2iw5b1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
超家族 Superfamily superfamily	a.4.1 — Homeodomain-like
家族 Family family	a.4.1.3 — Myb/SANT domain

结构域编号 domain_id	d2iw5b2
类 Class class	h — Coiled coil proteins
折叠类型 Fold fold	h.1 — Parallel coiled-coil
超家族 Superfamily superfamily	h.1.35 — Demethylase interaction domain of CoREST
家族 Family family	h.1.35.1 — Demethylase interaction domain of CoREST

CATH v4.4 (3 domains)

结构域编号 domain_id	2iw5A01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	10 — Arc Repressor Mutant, subunit A
同源超家族 H-superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

结构域编号 domain_id	2iw5A03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	80 — ATP synthase, gamma subunit, helix hairpin domain

结构域编号 domain_id	2iw5B00
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily	1880 —

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7. 引用文献 (1)

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晶胞边长 a length_a	120.354 Å
晶胞边长 b length_b	178.222 Å
晶胞边长 c length_c	234.932 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	I 2 2 2
空间群编号 int_tables_number	23
晶系 crystal_system	—

分辨率 resolution	2.570 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2040
R_work r_work	0.2030
R_free r_free	0.2120

fit	/app/data/saxs_computation/iw/2iw5/2iw5.fit
pddf	/app/data/pr_computation/iw/2iw5/2iw5.pr.out
profile	/app/data/saxs_computation/iw/2iw5/2iw5.dat

Structural Basis for CoREST-Dependent Demethylation of Nucleosomes by the Human LSD1 Histone Demethylase

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 (7)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 water

6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (5 domains)

CATH v4.4 (3 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)