SAXSdb — 8sdb

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8sdb
沉积日期 deposition_date	2023-04-06
结构标题 title	Crystal Structure of E.Coli Branching Enzyme in complex with malto-octose
关键词 keywords	branching enzyme, starch, E. coli branching enzyme, SUGAR BINDING PROTEIN, TRANSFERASE-CARBOHYDRATE complex; TRANSFERASE/CARBOHYDRATE
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	46.28 Å
回转半径 Rg (电子) rg_electron	45.70 Å
零角强度 I(0) i0	1106720000.00
分子量 molecular_weight	273560.0 kDa
排除体积 excluded_volume	340160 Å³
包络体积 envelope_volume	437860 Å³
水化壳体积 shell_volume	78331 Å³
包络直径 envelope_diameter	149.9 Å
壳层 Rg shell_rg	51.44 Å
包络 Rg envelope_rg	45.23 Å
形状 Rg shape_rg	45.68 Å
总 Rg total_rg	45.97 Å
总原子数 total_atoms	19380
残基数 n_residues	2291
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	150.4 Å
Rg (实空间) rg_real	46.17 Å
Rg 误差 (实空间) rg_real_error	1.18 Å
I(0) (实空间) i0_real	1.1070e+09
I(0) 误差 (实空间) i0_real_error	1.9210e+07
Rg (倒空间) rg_reciprocal	46.28 Å
I(0) (倒空间) i0_reciprocal	1107000000.0000
解质量估计 total_estimate	0.9016
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	53.1 Å
偏度 Skewness skewness	0.195
峰度 Kurtosis kurtosis	-0.680
角度范围 angular_range	— – 0.1700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	134200000.0000
实空间数据点数 n_real_points	35
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.922; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.953

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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	1,4-alpha-glucan branching enzyme GlgB
分子量 formula_weight	71334.7 kDa
EC 编号 ec_number	2.4.1.18
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	19380

GTHLRPYETLGAHADTMDGVTGTRFSVWAPNARRVSVVGQFNYWDGRRHPMRLRKESGIWELFIPGAHNGQLYKYEMIDANGNLRLKSDPYAFEAQMRPETASLICGLPEKVVQTEERKKANQFDAPISIYEVHLGSWRRHTDNNFWLSYRELADQLVPYAKWMGFTHLELLPINEHPFDGSWGYQPTGLYAPTRRFGTRDDFRYFIDAAHAAGLNVILDWVPGHFPTDDFALAEFDGTNLYEHSDPREGYHQDWNTLIYNYGRREVSNFLVGNALYWIERFGIDALRVDAVASMIYRDYSRKEGEWIPNEFGGRENLEAIEFLRNTNRILGEQVSGAVTMAEESTDFPGVSRPQDMGGLGFWYKWNLGWMHDTLDYMKLDPVYRQYHHDKLTFGILYNYTENFVLPLSHDEVVHGKKSILDRMPGDAWQKFANLRAYYGWMWAFPGKKLLFMGNEFAQGREWNHDASLDWHLLEGGDNWHHGVQRLVRDLNLTYRHHKAMHELDFDPYGFEWLVVDDKERSVLIFVRRDKEGNEIIVASNFTPVPRHDYRFGINQPGKWREILNTDSMHYHGSNAGNGGTVHSDEIASHGRQHSLSLTLPPLATIWLVREAE

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 branched

描述 description	;alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose ;
分子量 formula_weight	828.7 kDa
来源方法 src_method	nat
拷贝数 entity_count	3

Entity 3 branched

描述 description	alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
分子量 formula_weight	666.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

Entity 4 branched

描述 description	alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
分子量 formula_weight	504.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

Entity 5 branched

描述 description	;alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose ;
分子量 formula_weight	1153.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

Entity 6 branched

描述 description	alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
分子量 formula_weight	342.3 kDa
来源方法 src_method	nat
拷贝数 entity_count	3

Entity 7 non-polymer

描述 description	alpha-D-glucopyranose
分子量 formula_weight	180.2 kDa
来源方法 src_method	nat
拷贝数 entity_count	6

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6. 折叠分类 (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

结构域编号 domain_id	8sdbA01
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	10 — Immunoglobulins

结构域编号 domain_id	8sdbA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	80 — Glycosidases

结构域编号 domain_id	8sdbA03
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	1180 — Golgi alpha-mannosidase II

结构域编号 domain_id	8sdbB01
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	10 — Immunoglobulins

结构域编号 domain_id	8sdbB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	80 — Glycosidases

结构域编号 domain_id	8sdbB03
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	1180 — Golgi alpha-mannosidase II

结构域编号 domain_id	8sdbC01
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	10 — Immunoglobulins

结构域编号 domain_id	8sdbC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	80 — Glycosidases

结构域编号 domain_id	8sdbC03
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	1180 — Golgi alpha-mannosidase II

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7. 引用文献 (1)

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晶胞边长 a length_a	146.489 Å
晶胞边长 b length_b	146.489 Å
晶胞边长 c length_c	294.920 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	120.00 °
晶胞分子数 Z z_pdb	24

空间群 space_group	P 32 2 1
空间群编号 int_tables_number	154
晶系 crystal_system	trigonal

分辨率 resolution	3.000 Å
最低分辨率 resolution_low	38.850 Å
R 因子 r_factor	0.2189
R_work r_work	0.2138
R_free r_free	0.3154

fit	/app/data/saxs_computation/sd/8sdb/8sdb.fit
pddf	/app/data/pr_computation/sd/8sdb/8sdb.pr.out
profile	/app/data/saxs_computation/sd/8sdb/8sdb.dat

Crystal Structure of E.Coli Branching Enzyme in complex with malto-octose

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution