SAXSdb — 1hmw

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1hmw
沉积日期 deposition_date	2000-12-05
结构标题 title	ACTIVE SITE OF CHONDROITINASE AC LYASE REVEALED BY THE STRUCTURE OF ENZYME-OLIGOSACCHARIDE COMPLEXES AND MUTAGENESIS
关键词 keywords	protein-oligosaccharide complex, active site, catalysis, 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	28.08 Å
回转半径 Rg (电子) rg_electron	27.48 Å
零角强度 I(0) i0	96908400.00
分子量 molecular_weight	78282.0 kDa
排除体积 excluded_volume	98152 Å³
包络体积 envelope_volume	117160 Å³
水化壳体积 shell_volume	35488 Å³
包络直径 envelope_diameter	101.8 Å
壳层 Rg shell_rg	35.03 Å
包络 Rg envelope_rg	27.77 Å
形状 Rg shape_rg	27.44 Å
总 Rg total_rg	28.32 Å
总原子数 total_atoms	5528
残基数 n_residues	674
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	96.8 Å
Rg (实空间) rg_real	28.12 Å
Rg 误差 (实空间) rg_real_error	0.88 Å
I(0) (实空间) i0_real	9.6910e+07
I(0) 误差 (实空间) i0_real_error	1.5340e+06
Rg (倒空间) rg_reciprocal	28.11 Å
I(0) (倒空间) i0_reciprocal	96910000.0000
解质量估计 total_estimate	0.8593
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	32.8 Å
偏度 Skewness skewness	0.442
峰度 Kurtosis kurtosis	-0.171
角度范围 angular_range	— – 0.2800 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	19480000.0000
实空间数据点数 n_real_points	57
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.741; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.978

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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	CHONDROITINASE AC
分子量 formula_weight	79797.7 kDa
EC 编号 ec_number	4.2.2.5
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	5854

MKKLFVTCIVFFSILSPALLIAQQTGTAELIMKRVMLDLKKPLRNMDKVAEKNLNTLQPDGSWKDVPYKDDAMTNWLPNNHLLQLETIIQAYIEKDSHYYGDDKVFDQISKAFKYWYDSDPKSRNWWHNEIATPQALGEMLILMRYGKKPLDEALVHKLTERMKRGEPEKKTGANKTDIALHYFYRALLTSDEALLSFAVKELFYPVQFVHYEEGLQYDYSYLQHGPQLQISSYGAVFITGVLKLANYVRDTPYALSTEKLAIFSKYYRDSYLKAIRGSYMDFNVEGRGVSRPDILNKKAEKKRLLVAKMIDLKHTEEWADAIARTDSTVAAGYKIEPYHHQFWNGDYVQHLRPAYSFNVRMVSKRTRRSESGNKENLLGRYLSDGATNIQLRGPEYYNIMPVWEWDKIPGITSRDYLTDRPLTKLWGEQGSNDFAGGVSDGVYGASAYALDYDSLQAKKAWFFFDKEIVCLGAGINSNAPENITTTLNQSWLNGPVISTAGKTGRGKITTFKAQGQFWLLHDAIGYYFPEGANLSLSTQSQKGNWFHINNSHSKDEVSGDVFKLWINHGARPENAQYAYIVLPGINKPEEIKKYNGTAPKVLANTNQLQAVYHQQLDMVQAIFYTAGKLSVAGIEIETDKPCAVLIKHINGKQVIWAADPLQKEKTAVLSIRDLKTGKTNRVKIDFPQQEFAGATVELK

来源 Source

来源生物 organism	Pedobacter heparinus
NCBI 分类编号 ncbi_taxonomy_id	984
宿主生物 host_organism	Pedobacter heparinus

Entity 2 branched

描述 description	;2-O-methyl-beta-L-fucopyranose-(1-4)-beta-D-xylopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-2)-[alpha-L-rhamnopyranose-(1-4)]alpha-D-mannopyranose ;
分子量 formula_weight	794.7 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 branched

描述 description	alpha-D-glucopyranuronic acid-(1-2)-[alpha-L-rhamnopyranose-(1-4)]alpha-D-mannopyranose
分子量 formula_weight	502.4 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 4 branched

描述 description	;4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-6-O-sulfo-beta-D-galactopyranose ;
分子量 formula_weight	918.8 kDa
来源方法 src_method	man
拷贝数 entity_count	1

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	1

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	326

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6. 折叠分类 (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

结构域编号 domain_id	d1hmwa1
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	d1hmwa2
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	d1hmwa3
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 (3 domains)

结构域编号 domain_id	1hmwA01
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	1hmwA02
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	1hmwA03
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

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7. 引用文献 (1)

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晶胞边长 a length_a	86.900 Å
晶胞边长 b length_b	86.900 Å
晶胞边长 c length_c	192.300 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	P 43 21 2
空间群编号 int_tables_number	96
晶系 crystal_system	—

分辨率 resolution	2.300 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	—
R_work r_work	0.2190
R_free r_free	0.2750

fit	/app/data/saxs_computation/hm/1hmw/1hmw.fit
pddf	/app/data/pr_computation/hm/1hmw/1hmw.pr.out
profile	/app/data/saxs_computation/hm/1hmw/1hmw.dat

ACTIVE SITE OF CHONDROITINASE AC LYASE REVEALED BY THE STRUCTURE OF ENZYME-OLIGOSACCHARIDE COMPLEXES AND MUTAGENESIS

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution