1jz3

E. COLI (lacZ) BETA-GALACTOSIDASE-TRAPPED 2-DEOXY-GALACTOSYL ENZYME INTERMEDIATE

Method: X-RAY DIFFRACTION D_max: 174.4 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	1jz3
沉积日期 deposition_date	2001-09-13
结构标题 title	E. COLI (lacZ) BETA-GALACTOSIDASE-TRAPPED 2-DEOXY-GALACTOSYL ENZYME INTERMEDIATE
关键词 keywords	TIM BARREL (ALPHA/BETA BARREL), JELLY-ROLL BARREL, IMMUNOGLOBULIN, BETA SUPERSANDWICH, HYDROLASE; HYDROLASE
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	52.04 Å
回转半径 Rg (电子) rg_electron	51.68 Å
零角强度 I(0) i0	3308910000.00
分子量 molecular_weight	470890.0 kDa
排除体积 excluded_volume	583110 Å³
包络体积 envelope_volume	754740 Å³
水化壳体积 shell_volume	116260 Å³
包络直径 envelope_diameter	184.8 Å
壳层 Rg shell_rg	59.16 Å
包络 Rg envelope_rg	51.23 Å
形状 Rg shape_rg	51.68 Å
总 Rg total_rg	51.87 Å
总原子数 total_atoms	33069
残基数 n_residues	4044
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	174.4 Å
Rg (实空间) rg_real	51.95 Å
Rg 误差 (实空间) rg_real_error	1.39 Å
I(0) (实空间) i0_real	3.3090e+09
I(0) 误差 (实空间) i0_real_error	6.0500e+07
Rg (倒空间) rg_reciprocal	52.11 Å
I(0) (倒空间) i0_reciprocal	3310000000.0000
解质量估计 total_estimate	0.8690
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	63.9 Å
偏度 Skewness skewness	0.307
峰度 Kurtosis kurtosis	-0.182
角度范围 angular_range	— – 0.1500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	509900000.0000
实空间数据点数 n_real_points	31
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.832; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.825

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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	Beta-Galactosidase
分子量 formula_weight	116506.3 kDa
EC 编号 ec_number	3.2.1.23
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	37369

GSHMLEDPVVLQRRDWENPGVTQLNRLAAHPPFASWRNSEEARTDRPSQQLRSLNGEWRFAWFPAPEAVPESWLECDLPEADTVVVPSNWQMHGYDAPIYTNVTYPITVNPPFVPTENPTGCYSLTFNVDESWLQEGQTRIIFDGVNSAFHLWCNGRWVGYGQDSRLPSEFDLSAFLRAGENRLAVMVLRWSDGSYLEDQDMWRMSGIFRDVSLLHKPTTQISDFHVATRFNDDFSRAVLEAEVQMCGELRDYLRVTVSLWQGETQVASGTAPFGGEIIDERGGYADRVTLRLNVENPKLWSAEIPNLYRAVVELHTADGTLIEAEACDVGFREVRIENGLLLLNGKPLLIRGVNRHEHHPLHGQVMDEQTMVQDILLMKQNNFNAVRCSHYPNHPLWYTLCDRYGLYVVDEANIETHGMVPMNRLTDDPRWLPAMSERVTRMVQRDRNHPSVIIWSLGNESGHGANHDALYRWIKSVDPSRPVQYEGGGADTTATDIICPMYARVDEDQPFPAVPKWSIKKWLSLPGETRPLILCEYAHAMGNSLGGFAKYWQAFRQYPRLQGGFVWDWVDQSLIKYDENGNPWSAYGGDFGDTPNDRQFCMNGLVFADRTPHPALTEAKHQQQFFQFRLSGQTIEVTSEYLFRHSDNELLHWMVALDGKPLASGEVPLDVAPQGKQLIELPELPQPESAGQLWLTVRVVQPNATAWSEAGHISAWQQWRLAENLSVTLPAASHAIPHLTTSEMDFCIELGNKRWQFNRQSGFLSQMWIGDKKQLLTPLRDQFTRAPLDNDIGVSEATRIDPNAWVERWKAAGHYQAEAALLQCTADTLADAVLITTAHAWQHQGKTLFISRKTYRIDGSGQMAITVDVEVASDTPHPARIGLNCQLAQVAERVNWLGLGPQENYPDRLTAACFDRWDLPLSDMYTPYVFPSENGLRCGTRELNYGPHQWRGDFQFNISRYSQQQLMETSHRHLLHAEEGTWLNIDGFHMGIGGDDSWSPSVSAEFQLSAGRYHYQLVWCQK

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 non-polymer

描述 description	2-deoxy-alpha-D-galactopyranose
分子量 formula_weight	164.2 kDa
来源方法 src_method	man
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	17

Entity 4 non-polymer

描述 description	SODIUM ION
分子量 formula_weight	23.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	16

Entity 5 non-polymer

描述 description	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
分子量 formula_weight	209.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 6 non-polymer

描述 description	DIMETHYL SULFOXIDE
分子量 formula_weight	78.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	110

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	4294

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6. 折叠分类 (SCOP + CATH) 40 domains

SCOP 2.08 (20 domains)

结构域编号 domain_id	d1jz3a1
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.1.4 — beta-Galactosidase/glucuronidase domain
家族 Family family	b.1.4.1 — beta-Galactosidase/glucuronidase domain

结构域编号 domain_id	d1jz3a2
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.1.4 — beta-Galactosidase/glucuronidase domain
家族 Family family	b.1.4.1 — beta-Galactosidase/glucuronidase domain

结构域编号 domain_id	d1jz3a3
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.18 — Galactose-binding domain-like
超家族 Superfamily superfamily	b.18.1 — Galactose-binding domain-like
家族 Family family	b.18.1.5 — beta-Galactosidase/glucuronidase, N-terminal domain

结构域编号 domain_id	d1jz3a4
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.30 — Supersandwich
超家族 Superfamily superfamily	b.30.5 — Galactose mutarotase-like
家族 Family family	b.30.5.1 — beta-Galactosidase, domain 5

结构域编号 domain_id	d1jz3a5
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.1.8.3 — beta-glycanases

结构域编号 domain_id	d1jz3b1
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.1.4 — beta-Galactosidase/glucuronidase domain
家族 Family family	b.1.4.1 — beta-Galactosidase/glucuronidase domain

结构域编号 domain_id	d1jz3b2
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.1.4 — beta-Galactosidase/glucuronidase domain
家族 Family family	b.1.4.1 — beta-Galactosidase/glucuronidase domain

结构域编号 domain_id	d1jz3b3
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.18 — Galactose-binding domain-like
超家族 Superfamily superfamily	b.18.1 — Galactose-binding domain-like
家族 Family family	b.18.1.5 — beta-Galactosidase/glucuronidase, N-terminal domain

结构域编号 domain_id	d1jz3b4
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.30 — Supersandwich
超家族 Superfamily superfamily	b.30.5 — Galactose mutarotase-like
家族 Family family	b.30.5.1 — beta-Galactosidase, domain 5

结构域编号 domain_id	d1jz3b5
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.1.8.3 — beta-glycanases

结构域编号 domain_id	d1jz3c1
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.1.4 — beta-Galactosidase/glucuronidase domain
家族 Family family	b.1.4.1 — beta-Galactosidase/glucuronidase domain

结构域编号 domain_id	d1jz3c2
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.1.4 — beta-Galactosidase/glucuronidase domain
家族 Family family	b.1.4.1 — beta-Galactosidase/glucuronidase domain

结构域编号 domain_id	d1jz3c3
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.18 — Galactose-binding domain-like
超家族 Superfamily superfamily	b.18.1 — Galactose-binding domain-like
家族 Family family	b.18.1.5 — beta-Galactosidase/glucuronidase, N-terminal domain

结构域编号 domain_id	d1jz3c4
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.30 — Supersandwich
超家族 Superfamily superfamily	b.30.5 — Galactose mutarotase-like
家族 Family family	b.30.5.1 — beta-Galactosidase, domain 5

结构域编号 domain_id	d1jz3c5
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.1.8.3 — beta-glycanases

结构域编号 domain_id	d1jz3d1
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.1.4 — beta-Galactosidase/glucuronidase domain
家族 Family family	b.1.4.1 — beta-Galactosidase/glucuronidase domain

结构域编号 domain_id	d1jz3d2
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.1.4 — beta-Galactosidase/glucuronidase domain
家族 Family family	b.1.4.1 — beta-Galactosidase/glucuronidase domain

结构域编号 domain_id	d1jz3d3
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.18 — Galactose-binding domain-like
超家族 Superfamily superfamily	b.18.1 — Galactose-binding domain-like
家族 Family family	b.18.1.5 — beta-Galactosidase/glucuronidase, N-terminal domain

结构域编号 domain_id	d1jz3d4
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.30 — Supersandwich
超家族 Superfamily superfamily	b.30.5 — Galactose mutarotase-like
家族 Family family	b.30.5.1 — beta-Galactosidase, domain 5

结构域编号 domain_id	d1jz3d5
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.1.8.3 — beta-glycanases

CATH v4.4 (20 domains)

结构域编号 domain_id	1jz3A01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	260 — Galactose-binding domain-like

结构域编号 domain_id	1jz3A02
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	1jz3A03
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	1jz3A04
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	1jz3A05
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	98 — Beta-galactosidase; Chain A, domain 5
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1jz3B01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	260 — Galactose-binding domain-like

结构域编号 domain_id	1jz3B02
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	1jz3B03
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	1jz3B04
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	1jz3B05
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	98 — Beta-galactosidase; Chain A, domain 5
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1jz3C01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	260 — Galactose-binding domain-like

结构域编号 domain_id	1jz3C02
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	1jz3C03
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	1jz3C04
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	1jz3C05
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	98 — Beta-galactosidase; Chain A, domain 5
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	1jz3D01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	120 — Jelly Rolls
同源超家族 H-superfamily homologous superfamily	260 — Galactose-binding domain-like

结构域编号 domain_id	1jz3D02
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	1jz3D03
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	1jz3D04
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	1jz3D05
类 Class class	2 — Mainly Beta
架构 Architecture architecture	70 — Distorted Sandwich
拓扑 Topology topology	98 — Beta-galactosidase; Chain A, domain 5
同源超家族 H-superfamily homologous superfamily	10 —

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7. 引用文献 (5)

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晶胞边长 a length_a	149.560 Å
晶胞边长 b length_b	168.190 Å
晶胞边长 c length_c	200.690 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	16

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	1.750 Å
最低分辨率 resolution_low	16.000 Å
R 因子 r_factor	—
R_work r_work	0.1580
R_free r_free	0.2220