SAXSdb — 1lxm

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1lxm
沉积日期 deposition_date	2002-06-05
结构标题 title	Crystal Structure of Streptococcus agalactiae Hyaluronate Lyase Complexed with Hexasaccharide Unit of Hyaluronan
关键词 keywords	Streptococcus agalactiae, Protein-carbohydrate complex, hyaluronan, 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	30.98 Å
回转半径 Rg (电子) rg_electron	30.84 Å
零角强度 I(0) i0	133072000.00
分子量 molecular_weight	91331.0 kDa
排除体积 excluded_volume	114050 Å³
包络体积 envelope_volume	138900 Å³
水化壳体积 shell_volume	38528 Å³
包络直径 envelope_diameter	117.4 Å
壳层 Rg shell_rg	36.87 Å
包络 Rg envelope_rg	31.16 Å
形状 Rg shape_rg	30.82 Å
总 Rg total_rg	31.40 Å
总原子数 total_atoms	6437
残基数 n_residues	794
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	109.2 Å
Rg (实空间) rg_real	31.17 Å
Rg 误差 (实空间) rg_real_error	0.97 Å
I(0) (实空间) i0_real	1.3310e+08
I(0) 误差 (实空间) i0_real_error	2.1570e+06
Rg (倒空间) rg_reciprocal	31.09 Å
I(0) (倒空间) i0_reciprocal	133100000.0000
解质量估计 total_estimate	0.8284
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	34.2 Å
偏度 Skewness skewness	0.591
峰度 Kurtosis kurtosis	0.031
角度范围 angular_range	— – 0.2550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	26720000.0000
实空间数据点数 n_real_points	52
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.672; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.869; Smooth: 0.880

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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 (3)

Entity 1 polymer

描述 description	HYALURONATE Lyase
分子量 formula_weight	92510.3 kDa
EC 编号 ec_number	4.2.2.1
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	6628

SEHPQPVTTQIEKSVNTALNKNYVFNKADYQYTLTNPSLGKIVGGILYPNATGSTTVKISDKSGKIIKEVPLSVTASTEDNFTKLLDKWNDVTIGNYVYDTNDSNMQKLNQKLDETNAKNIEAIKLDSNRTFLWKDLDNLNNSAQLTATYRRLEDLAKQITNPHSTIYKNEKAIRTVKESLAWLHQNFYNVNKDIEGSANWWDFEIGVPRSITGTLSLMNNYFTDAEIKTYTDPIEHFVPDAEYFRKTLVNPFKALGGNLVDMGRVKIIEGLLRKDNTIIEKTSHSLKNLFTTATKAEGFYADGSYIDHTNVAYTGAYGNVLIDGLTQLLPIIQETDYKISNQELDMVYKWINQSFLPLIVKGELMDMSRGRSISREAASSHAAAVEVLRGFLRLANMSNEERNLDLKSTIKTIITSNKFYNVFNNLKSYSDIANMNKLLNDSTVATKPLKSNLSTFNSMDRLAYYNAKKDFGFALSLHSKRTLNYEGMNDENTRGWYTGDGMFYIYNSDQSHYSNHFWPTVNPYKMAGTTEKDAKREDTTKEFMSKHSKDAKEKTGQVTGTSDFVGSVKLNDHFALAAMDFTNWDRTLTAQKGWVILNDKIVFLGSNIKNTNGIGNVSTTIDQRKDDSKTPYTTYVNGKTIDLKQASSQQFTDTKSVFLESKEPGRNIGYIFFKNSTIDIERKEQTGTWNSINRTSKNTSIVSNPFITISQKHDNKGDSYGYMMVPNIDRTSFDKLANSKEVELLENSSKQQVIYDKNSQTWAVIKHDNQESLINNQFKMNKAGLYLVQKVGNDYQNVYYQPQTMTKTDQLAI

来源 Source

来源生物 organism	Streptococcus agalactiae
NCBI 分类编号 ncbi_taxonomy_id	1311
宿主生物 host_organism	Escherichia coli

Entity 2 branched

描述 description	;beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	1156.0 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 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	191

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1lxma1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.102 — alpha/alpha toroid
超家族 Superfamily superfamily	a.102.3 — Chondroitin AC/alginate lyase
家族 Family family	a.102.3.2 — Hyaluronate lyase-like catalytic, N-terminal domain

结构域编号 domain_id	d1lxma2
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	d1lxma3
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.24 — Hyaluronate lyase-like, C-terminal domain
超家族 Superfamily superfamily	b.24.1 — Hyaluronate lyase-like, C-terminal domain
家族 Family family	b.24.1.1 — Hyaluronate lyase-like, C-terminal domain

结构域编号 domain_id	d1lxma4
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.30.5.2 — Hyaluronate lyase-like, central domain

CATH v4.4 (4 domains)

结构域编号 domain_id	1lxmA01
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	1lxmA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	50 — Alpha/alpha barrel
拓扑 Topology topology	10 — Glycosyltransferase
同源超家族 H-superfamily homologous superfamily	100 — Chondroitin AC/alginate lyase

结构域编号 domain_id	1lxmA03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	220 — Chondroitinase Ac; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Polysaccharide lyase family 8-like, C-terminal

结构域编号 domain_id	1lxmA04
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	1380 — E set domains; domain 4

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7. 引用文献 (1)

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晶胞边长 a length_a	51.108 Å
晶胞边长 b length_b	155.043 Å
晶胞边长 c length_c	238.136 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	8

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	2.200 Å
最低分辨率 resolution_low	50.000 Å
R 因子 r_factor	0.2180
R_work r_work	0.2180
R_free r_free	0.2710

fit	/app/data/saxs_computation/lx/1lxm/1lxm.fit
pddf	/app/data/pr_computation/lx/1lxm/1lxm.pr.out
profile	/app/data/saxs_computation/lx/1lxm/1lxm.dat

Crystal Structure of Streptococcus agalactiae Hyaluronate Lyase Complexed with Hexasaccharide Unit of Hyaluronan

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution