SAXSdb — 1ibv

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1ibv
沉积日期 deposition_date	2001-03-29
结构标题 title	STRUCTURE OF THE D53,54N MUTANT OF HISTIDINE DECARBOXYLASE BOUND WITH HISTIDINE METHYL ESTER AT-170 C
关键词 keywords	SUBSTRATE-INDUCED ACTIVATION, ACTIVE FORM, SITE-DIRECTED MUTANT, PYRUVOYL, CARBOXY-LYASE, LYASE; 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	27.93 Å
回转半径 Rg (电子) rg_electron	26.70 Å
零角强度 I(0) i0	172980000.00
分子量 molecular_weight	102720.0 kDa
排除体积 excluded_volume	127890 Å³
包络体积 envelope_volume	148590 Å³
水化壳体积 shell_volume	43252 Å³
包络直径 envelope_diameter	80.8 Å
壳层 Rg shell_rg	36.40 Å
包络 Rg envelope_rg	26.84 Å
形状 Rg shape_rg	26.70 Å
总 Rg total_rg	27.64 Å
总原子数 total_atoms	7224
残基数 n_residues	927
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	80.0 Å
Rg (实空间) rg_real	27.66 Å
Rg 误差 (实空间) rg_real_error	0.39 Å
I(0) (实空间) i0_real	1.7300e+08
I(0) 误差 (实空间) i0_real_error	2.2850e+06
Rg (倒空间) rg_reciprocal	27.74 Å
I(0) (倒空间) i0_reciprocal	173000000.0000
解质量估计 total_estimate	0.9081
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	36.5 Å
偏度 Skewness skewness	0.019
峰度 Kurtosis kurtosis	-0.563
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	25710000.0000
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: 0.962; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.947

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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	HISTIDINE DECARBOXYLASE BETA CHAIN
分子量 formula_weight	8848.9 kDa
突变 mutation	D53N, D54N
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,C,E
原子数 atom_count	7332

SELDAKLNKLGVDRIAISPYKQWTRGYMEPGNIGNGYVTGLKVDAGVRDKSDNNVLDGIVSYDRAETKNAYIGQINMTTAS

来源 Source

来源生物 organism	Lactobacillus sp. 30A
NCBI 分类编号 ncbi_taxonomy_id	1593
宿主生物 host_organism	Escherichia coli

Entity 2 polymer

描述 description	Histidine decarboxylase alpha chain
分子量 formula_weight	25285.4 kDa
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,D,F

XFTGVQGRVIGYDILRSPEVDKAKPLFTETQWDGSELPIYDAKPLQDALVEYFGTEQDRRHYPAPGSFIVCANKGVTAERPKNDADMKPGQGYGVWSAIAISFAKDPTKDSSMFVEDAGVWETPNEDELLEYLEGRRKAMAKSIAECGQDAHASFESSWIGFAYTMMEPGQIGNAITVAPYVSLPIDSIPGGSILTPDKDMEIMENLTMPEWLEKMGYKSLSANNALKY

来源 Source

来源生物 organism	Lactobacillus sp. 30A
NCBI 分类编号 ncbi_taxonomy_id	1593
宿主生物 host_organism	Escherichia coli

Entity 3 non-polymer

描述 description	HISTIDINE-METHYL-ESTER
分子量 formula_weight	170.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

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	108

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6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

结构域编号 domain_id	d1ibv.1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.155 — Pyruvoyl-dependent histidine and arginine decarboxylases
超家族 Superfamily superfamily	d.155.1 — Pyruvoyl-dependent histidine and arginine decarboxylases
家族 Family family	d.155.1.1 — Histidine decarboxylase

结构域编号 domain_id	d1ibv.2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.155 — Pyruvoyl-dependent histidine and arginine decarboxylases
超家族 Superfamily superfamily	d.155.1 — Pyruvoyl-dependent histidine and arginine decarboxylases
家族 Family family	d.155.1.1 — Histidine decarboxylase

结构域编号 domain_id	d1ibv.3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.155 — Pyruvoyl-dependent histidine and arginine decarboxylases
超家族 Superfamily superfamily	d.155.1 — Pyruvoyl-dependent histidine and arginine decarboxylases
家族 Family family	d.155.1.1 — Histidine decarboxylase

CATH v4.4 (3 domains)

结构域编号 domain_id	1ibvA00
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	510 — Pyruvoyl-Dependent Histidine Decarboxylas; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Pyruvoyl-Dependent Histidine Decarboxylas, subunit A

结构域编号 domain_id	1ibvC00
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	510 — Pyruvoyl-Dependent Histidine Decarboxylas; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Pyruvoyl-Dependent Histidine Decarboxylas, subunit A

结构域编号 domain_id	1ibvE00
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	510 — Pyruvoyl-Dependent Histidine Decarboxylas; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Pyruvoyl-Dependent Histidine Decarboxylas, subunit A

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7. 引用文献 (1)

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晶胞边长 a length_a	96.272 Å
晶胞边长 b length_b	115.480 Å
晶胞边长 c length_c	206.393 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	24

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	2.500 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2465
R_work r_work	0.2429
R_free r_free	0.2793

fit	/app/data/saxs_computation/ib/1ibv/1ibv.fit
pddf	/app/data/pr_computation/ib/1ibv/1ibv.pr.out
profile	/app/data/saxs_computation/ib/1ibv/1ibv.dat

STRUCTURE OF THE D53,54N MUTANT OF HISTIDINE DECARBOXYLASE BOUND WITH HISTIDINE METHYL ESTER AT-170 C

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

来源 Source

Entity 3 non-polymer

Entity 4 water

6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)