SAXSdb — 2j4g

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2j4g
沉积日期 deposition_date	2006-08-31
结构标题 title	Bacteroides thetaiotaomicron GH84 O-GlcNAcase in complex with n-butyl- thiazoline inhibitor
关键词 keywords	GH84, ENZYME, THIAZOLINE, INHIBITION, O-GLCNACASE, INHIBITOR; INHIBITOR
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	51.42 Å
回转半径 Rg (电子) rg_electron	51.35 Å
零角强度 I(0) i0	253672000.00
分子量 molecular_weight	134620.0 kDa
排除体积 excluded_volume	168850 Å³
包络体积 envelope_volume	252260 Å³
水化壳体积 shell_volume	40045 Å³
包络直径 envelope_diameter	158.2 Å
壳层 Rg shell_rg	58.82 Å
包络 Rg envelope_rg	48.62 Å
形状 Rg shape_rg	51.34 Å
总 Rg total_rg	51.62 Å
总原子数 total_atoms	9509
残基数 n_residues	1166
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	146.4 Å
Rg (实空间) rg_real	51.59 Å
Rg 误差 (实空间) rg_real_error	1.54 Å
I(0) (实空间) i0_real	2.5370e+08
I(0) 误差 (实空间) i0_real_error	4.7280e+06
Rg (倒空间) rg_reciprocal	51.24 Å
I(0) (倒空间) i0_reciprocal	253500000.0000
解质量估计 total_estimate	0.6751
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	28.3 Å
偏度 Skewness skewness	0.114
峰度 Kurtosis kurtosis	-1.171
角度范围 angular_range	— – 0.1550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	9770000.0000
实空间数据点数 n_real_points	32
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.418; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.518; Smooth: 0.000

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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	HYALURONOGLUCOSAMINIDASE
分子量 formula_weight	82188.0 kDa
EC 编号 ec_number	3.2.1.52
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	10075

NVSLQPPPQQLIVQNKTIDLPAVYQLNGGEEANPHAVKVLKELLSGKQSSKKGMLISIGEKGDKSVRKYSRQIPDHKEGYYLSVNEKEIVLAGNDERGTYYALQTFAQLLKDGKLPEVEIKDYPSVRYRGVVEGFYGTPWSHQARLSQLKFYGKNKMNTYIYGPKDDPYHSAPNWRLPYPDKEAAQLQELVAVANENEVDFVWAIHPGQDIKWNKEDRDLLLAKFEKMYQLGVRSFAVFFDDISGEGTNPQKQAELLNYIDEKFAQVKPDINQLVMCPTEYNKSWSNPNGNYLTTLGDKLNPSIQIMWTGDRVISDITRDGISWINERIKRPAYIWWNFPVSDYVRDHLLLGPVYGNDTTIAKEMSGFVTNPMEHAESSKIAIYSVASYAWNPAKYDTWQTWKDAIRTILPSAAEELECFAMHNSDLGPNGHGYRREESMDIQPAAERFLKAFKEGKNYDKADFETLQYTFERMKESADILLMNTENKPLIVEITPWVHQFKLTAEMGEEVLKMVEGRNESYFLRKYNHVKALQQQMFYIDQTSNQNPYQPGVKTATRVIKPLIDRTFATVVKFFNQKFNAHLDATTDYMPHKMISNVEQIKNLPLQVKANRVLISPANEVVKWAAGNSVEIELDAIYPGENIQINFGKDAPCTWGRLEISTDGKEWKTVDLKQKESRLSAGLQKAPVKFVRFTNVSDEEQQVYLRQFVLTIEKK

来源 Source

来源生物 organism	BACTEROIDES THETAIOTAOMICRON
NCBI 分类编号 ncbi_taxonomy_id	226186
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 non-polymer

描述 description	(3AR,5R,6S,7R,7AR)-5-(HYDROXYMETHYL)-2-PROPYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D][1,3]THIAZOLE-6,7-DIOL
分子量 formula_weight	247.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 non-polymer

描述 description	ACETATE ION
分子量 formula_weight	59.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	GLYCEROL
分子量 formula_weight	92.1 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	558

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6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d2j4ga1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.246 — Hyaluronidase domain-like
超家族 Superfamily superfamily	a.246.1 — Hyaluronidase post-catalytic domain-like
家族 Family family	a.246.1.1 — Hyaluronidase post-catalytic domain-like

结构域编号 domain_id	d2j4ga2
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.1.8.10 — alpha-D-glucuronidase/Hyaluronidase catalytic domain

结构域编号 domain_id	d2j4ga3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.92 — Zincin-like
超家族 Superfamily superfamily	d.92.2 — beta-N-acetylhexosaminidase-like domain
家族 Family family	d.92.2.3 — Hyaluronidase N-terminal domain-like

结构域编号 domain_id	d2j4gb1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.246 — Hyaluronidase domain-like
超家族 Superfamily superfamily	a.246.1 — Hyaluronidase post-catalytic domain-like
家族 Family family	a.246.1.1 — Hyaluronidase post-catalytic domain-like

结构域编号 domain_id	d2j4gb2
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.1.8.10 — alpha-D-glucuronidase/Hyaluronidase catalytic domain

结构域编号 domain_id	d2j4gb3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.92 — Zincin-like
超家族 Superfamily superfamily	d.92.2 — beta-N-acetylhexosaminidase-like domain
家族 Family family	d.92.2.3 — Hyaluronidase N-terminal domain-like

CATH v4.4 (6 domains)

结构域编号 domain_id	2j4gA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	379 — Chitobiase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Chitobiase/beta-hexosaminidase domain 2-like

结构域编号 domain_id	2j4gA02
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	2j4gA03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily	460 — Hyaluronidase post-catalytic domain-like

结构域编号 domain_id	2j4gB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	379 — Chitobiase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Chitobiase/beta-hexosaminidase domain 2-like

结构域编号 domain_id	2j4gB02
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	2j4gB03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily	460 — Hyaluronidase post-catalytic domain-like

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7. 引用文献 (2)

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晶胞边长 a length_a	185.106 Å
晶胞边长 b length_b	51.711 Å
晶胞边长 c length_c	172.782 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	100.11 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	2.250 Å
最低分辨率 resolution_low	169.030 Å
R 因子 r_factor	0.2230
R_work r_work	0.2200
R_free r_free	0.2840

fit	/app/data/saxs_computation/j4/2j4g/2j4g.fit
pddf	/app/data/pr_computation/j4/2j4g/2j4g.pr.out
profile	/app/data/saxs_computation/j4/2j4g/2j4g.dat

Bacteroides thetaiotaomicron GH84 O-GlcNAcase in complex with n-butyl- thiazoline inhibitor

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