1i7m

;HUMAN S-ADENOSYLMETHIONINE DECARBOXYLASE WITH COVALENTLY BOUND PYRUVOYL GROUP AND COMPLEXED WITH 4-AMIDINOINDAN-1-ONE-2'-AMIDINOHYDRAZONE ;

Method: X-RAY DIFFRACTION D_max: 93.4 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	1i7m
沉积日期 deposition_date	2001-03-09
结构标题 title	;HUMAN S-ADENOSYLMETHIONINE DECARBOXYLASE WITH COVALENTLY BOUND PYRUVOYL GROUP AND COMPLEXED WITH 4-AMIDINOINDAN-1-ONE-2'-AMIDINOHYDRAZONE ;
关键词 keywords	Spermidine biosynthesis, Lyase, Decarboxylase, Pyruvate, S-ADENOSYLMETHIONINE, SANDWICH, ALLOSTERIC ENZYME, PYRUVOYL; LYASE
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	27.79 Å
回转半径 Rg (电子) rg_electron	26.96 Å
零角强度 I(0) i0	83985100.00
分子量 molecular_weight	71857.0 kDa
排除体积 excluded_volume	89344 Å³
包络体积 envelope_volume	103650 Å³
水化壳体积 shell_volume	32138 Å³
包络直径 envelope_diameter	96.9 Å
壳层 Rg shell_rg	34.37 Å
包络 Rg envelope_rg	27.06 Å
形状 Rg shape_rg	26.93 Å
总 Rg total_rg	27.78 Å
总原子数 total_atoms	4982
残基数 n_residues	586
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	93.4 Å
Rg (实空间) rg_real	27.86 Å
Rg 误差 (实空间) rg_real_error	0.78 Å
I(0) (实空间) i0_real	8.3990e+07
I(0) 误差 (实空间) i0_real_error	1.3890e+06
Rg (倒空间) rg_reciprocal	27.84 Å
I(0) (倒空间) i0_reciprocal	83980000.0000
解质量估计 total_estimate	0.8648
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	29.5 Å
偏度 Skewness skewness	0.407
峰度 Kurtosis kurtosis	-0.445
角度范围 angular_range	— – 0.2850 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	30840000.0000
实空间数据点数 n_real_points	58
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.785; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.963; Smooth: 0.920

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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 (5)

Entity 1 polymer

描述 description	S-ADENOSYLMETHIONINE DECARBOXYLASE BETA CHAIN
分子量 formula_weight	7741.5 kDa
EC 编号 ec_number	4.1.1.50
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	B,D
原子数 atom_count	5225

MEAAHFFEGTEKLLEVWFSRQQPDANQGSGDLRTIPRSEWDILLKDVQCSIISVTKTDKQEAYVLSE

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	S-ADENOSYLMETHIONINE DECARBOXYLASE ALPHA CHAIN
分子量 formula_weight	31187.8 kDa
EC 编号 ec_number	4.1.1.50
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,C

XSMFVSKRRFILKTCGTTLLLKALVPLLKLARDYSGFDSIQSFFYSRKNFMKPSHQGYPHRNFQEEIEFLNAIFPNGAGYCMGRMNSDCWYLYTLDFPESRVISQPDQTLEILMSELDPAVMDQFYMKDGVTAKDVTRESGIRDLIPGSVIDATMFNPCGYSMNGMKSDGTYWTIHITPEPEFSYVSFETNLSQTSYDDLIRKVVEVFKPGKFVTTLFVNQSSKCRTVLASPQKIEGFKRLDCQSAMFNDYNFVFTSFAKKQQQQQS

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	1,4-DIAMINOBUTANE
分子量 formula_weight	88.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	4-AMIDINOINDAN-1-ONE-2'-AMIDINOHYDRAZONE
分子量 formula_weight	230.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 5 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	243

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6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1i7m.1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.156 — S-adenosylmethionine decarboxylase
超家族 Superfamily superfamily	d.156.1 — S-adenosylmethionine decarboxylase
家族 Family family	d.156.1.1 — S-adenosylmethionine decarboxylase

结构域编号 domain_id	d1i7m.2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.156 — S-adenosylmethionine decarboxylase
超家族 Superfamily superfamily	d.156.1 — S-adenosylmethionine decarboxylase
家族 Family family	d.156.1.1 — S-adenosylmethionine decarboxylase

CATH v4.4 (4 domains)

结构域编号 domain_id	1i7mA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	90 — S-adenosylmethionine decarboxylase
同源超家族 H-superfamily homologous superfamily	10 — S-adenosylmethionine decarboxylase

结构域编号 domain_id	1i7mB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
同源超家族 H-superfamily homologous superfamily	50 — S-adenosylmethionine decarboxylase

结构域编号 domain_id	1i7mC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	90 — S-adenosylmethionine decarboxylase
同源超家族 H-superfamily homologous superfamily	10 — S-adenosylmethionine decarboxylase

结构域编号 domain_id	1i7mD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
同源超家族 H-superfamily homologous superfamily	50 — S-adenosylmethionine decarboxylase

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7. 引用文献 (2)

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晶胞边长 a length_a	73.899 Å
晶胞边长 b length_b	55.672 Å
晶胞边长 c length_c	96.086 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	110.39 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	2.240 Å
最低分辨率 resolution_low	29.410 Å
R 因子 r_factor	—
R_work r_work	0.2420
R_free r_free	0.2940

fit	/app/data/saxs_computation/i7/1i7m/1i7m.fit
pddf	/app/data/pr_computation/i7/1i7m/1i7m.pr.out
profile	/app/data/saxs_computation/i7/1i7m/1i7m.dat

;HUMAN S-ADENOSYLMETHIONINE DECARBOXYLASE WITH COVALENTLY BOUND PYRUVOYL GROUP AND COMPLEXED WITH 4-AMIDINOINDAN-1-ONE-2'-AMIDINOHYDRAZONE ;

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 (5)

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 water

6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. 引用文献 (2)

8. 文件与曲线 (10)

Files (7)

Curves (3)