1uks

Crystal structure of F183L/F259L mutant cyclodextrin glucanotransferase complexed with a pseudo-maltotetraose derived from acarbose

Method: X-RAY DIFFRACTION D_max: 122.7 Å Quality: REASONABLE

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	1uks
沉积日期 deposition_date	2003-09-01
结构标题 title	Crystal structure of F183L/F259L mutant cyclodextrin glucanotransferase complexed with a pseudo-maltotetraose derived from acarbose
关键词 keywords	CGTASE, ACARBOSE, CARBOHYDRATE/PROTEIN INTERACTION, TRANSFERASE; TRANSFERASE
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	36.60 Å
回转半径 Rg (电子) rg_electron	35.98 Å
零角强度 I(0) i0	360228000.00
分子量 molecular_weight	151630.0 kDa
排除体积 excluded_volume	188270 Å³
包络体积 envelope_volume	229710 Å³
水化壳体积 shell_volume	53815 Å³
包络直径 envelope_diameter	125.0 Å
壳层 Rg shell_rg	42.20 Å
包络 Rg envelope_rg	35.40 Å
形状 Rg shape_rg	35.99 Å
总 Rg total_rg	36.34 Å
总原子数 total_atoms	10704
残基数 n_residues	1372
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	122.7 Å
Rg (实空间) rg_real	36.66 Å
Rg 误差 (实空间) rg_real_error	0.76 Å
I(0) (实空间) i0_real	3.6020e+08
I(0) 误差 (实空间) i0_real_error	5.2000e+06
Rg (倒空间) rg_reciprocal	36.62 Å
I(0) (倒空间) i0_reciprocal	360200000.0000
解质量估计 total_estimate	0.6533
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	39.9 Å
偏度 Skewness skewness	0.406
峰度 Kurtosis kurtosis	-0.328
角度范围 angular_range	— – 0.2150 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	69740000.0000
实空间数据点数 n_real_points	44
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.847; Stabil: 1.000; Sysdev: 0.048; Positv: 1.000; Valcen: 0.970; Smooth: 0.834

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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 (6)

Entity 1 polymer

描述 description	Cyclomaltodextrin glucanotransferase
分子量 formula_weight	75162.1 kDa
EC 编号 ec_number	2.4.1.19
突变 mutation	F183L/F259L
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,B
原子数 atom_count	11443

APDTSVSNKQNFSTDVIYQIFTDRFSDGNPANNPTGAAFDGSCTNLRLYCGGDWQGIINKINDGYLTGMGITAIWISQPVENIYSVINYSGVNNTAYHGYWARDFKKTNPAYGTMQDFKNLIDTAHAHNIKVIIDFAPNHTSPASSDDPSFAENGRLYDNGNLLGGYTNDTQNLFHHYGGTDLSTIENGIYKNLYDLADLNHNNSSVDVYLKDAIKMWLDLGVDGIRVDAVKHMPFGWQKSFMATINNYKPVFTFGEWLLGVNEISPEYHQFANESGMSLLDFRFAQKARQVFRDNTDNMYGLKAMLEGSEVDYAQVNDQVTFIDNHDMERFHTSNGDRRKLEQALAFTLTSRGVPAIYYGSEQYMSGGNDPDNRARLPSFSTTTTAYQVIQKLAPLRKSNPAIAYGSTHERWINNDVIIYERKFGNNVAVVAINRNMNTPASITGLVTSLPRGSYNDVLGGILNGNTLTVGAGGAASNFTLAPGGTAVWQYTTDATTPIIGNVGPMMAKPGVTITIDGRGFGSGKGTVYFGTTAVTGADIVAWEDTQIQVKIPAVPGGIYDIRVANAAGAASNIYDNFEVLTGDQVTVRFVINNATTALGQNVFLTGNVSELGNWDPNNAIGPMYNQVVYQYPTWYYDVSVPAGQTIEFKFLKKQGSTVTWEGGANRTFTTPTSGTATVNVNWQP

来源 Source

来源生物 organism	Bacillus sp.
NCBI 分类编号 ncbi_taxonomy_id	1410
宿主生物 host_organism	Escherichia coli

Entity 2 branched

描述 description	4,6-dideoxy-alpha-D-xylo-hexopyranose-(1-4)-beta-D-galactopyranose
分子量 formula_weight	310.3 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	alpha-D-glucopyranose
分子量 formula_weight	180.2 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL
分子量 formula_weight	175.2 kDa
来源方法 src_method	man
拷贝数 entity_count	2

Entity 5 non-polymer

描述 description	CALCIUM ION
分子量 formula_weight	40.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 6 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	739

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1uksa1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.18 — E set domains
家族 Family family	b.1.18.2 — E-set domains of sugar-utilizing enzymes

结构域编号 domain_id	d1uksa2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.3 — Prealbumin-like
超家族 Superfamily superfamily	b.3.1 — Starch-binding domain-like
家族 Family family	b.3.1.1 — Starch-binding domain

结构域编号 domain_id	d1uksa3
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.71 — Glycosyl hydrolase domain
超家族 Superfamily superfamily	b.71.1 — Glycosyl hydrolase domain
家族 Family family	b.71.1.1 — alpha-Amylases, C-terminal beta-sheet domain

结构域编号 domain_id	d1uksa4
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.8 — (Trans)glycosidases
家族 Family family	c.1.8.1 — Amylase, catalytic domain

结构域编号 domain_id	d1uksb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.1 — Immunoglobulin-like beta-sandwich
超家族 Superfamily superfamily	b.1.18 — E set domains
家族 Family family	b.1.18.2 — E-set domains of sugar-utilizing enzymes

结构域编号 domain_id	d1uksb2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.3 — Prealbumin-like
超家族 Superfamily superfamily	b.3.1 — Starch-binding domain-like
家族 Family family	b.3.1.1 — Starch-binding domain

结构域编号 domain_id	d1uksb3
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.71 — Glycosyl hydrolase domain
超家族 Superfamily superfamily	b.71.1 — Glycosyl hydrolase domain
家族 Family family	b.71.1.1 — alpha-Amylases, C-terminal beta-sheet domain

结构域编号 domain_id	d1uksb4
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.8 — (Trans)glycosidases
家族 Family family	c.1.8.1 — Amylase, catalytic domain

CATH v4.4 (8 domains)

结构域编号 domain_id	1uksA01
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	1uksA02
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	1uksA03
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	1uksA04
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	1uksB01
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	1uksB02
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	1uksB03
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	1uksB04
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

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7. 引用文献 (2)

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晶胞边长 a length_a	64.850 Å
晶胞边长 b length_b	74.530 Å
晶胞边长 c length_c	78.940 Å
晶胞夹角 α angle_alpha	85.19 °
晶胞夹角 β angle_beta	104.86 °
晶胞夹角 γ angle_gamma	101.04 °
晶胞分子数 Z z_pdb	2

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

分辨率 resolution	1.900 Å
最低分辨率 resolution_low	10.000 Å
R 因子 r_factor	0.1650
R_work r_work	0.1620
R_free r_free	0.2150

fit	/app/data/saxs_computation/uk/1uks/1uks.fit
pddf	/app/data/pr_computation/uk/1uks/1uks.pr.out
profile	/app/data/saxs_computation/uk/1uks/1uks.dat