1ofm

CRYSTAL STRUCTURE OF CHONDROITINASE B COMPLEXED TO CHONDROITIN 4-SULFATE TETRASACCHARIDE

Method: X-RAY DIFFRACTION D_max: 77.4 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	1ofm
沉积日期 deposition_date	2003-04-15
结构标题 title	CRYSTAL STRUCTURE OF CHONDROITINASE B COMPLEXED TO CHONDROITIN 4-SULFATE TETRASACCHARIDE
关键词 keywords	ACTIVE SITE, BETA-ELIMINATION, CHONDROITIN 4-SULFATE, 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	23.40 Å
回转半径 Rg (电子) rg_electron	22.70 Å
零角强度 I(0) i0	51744600.00
分子量 molecular_weight	55659.0 kDa
排除体积 excluded_volume	69511 Å³
包络体积 envelope_volume	79748 Å³
水化壳体积 shell_volume	28558 Å³
包络直径 envelope_diameter	78.9 Å
壳层 Rg shell_rg	30.55 Å
包络 Rg envelope_rg	23.12 Å
形状 Rg shape_rg	22.68 Å
总 Rg total_rg	23.65 Å
总原子数 total_atoms	3919
残基数 n_residues	480
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	77.4 Å
Rg (实空间) rg_real	23.33 Å
Rg 误差 (实空间) rg_real_error	0.58 Å
I(0) (实空间) i0_real	5.1740e+07
I(0) 误差 (实空间) i0_real_error	7.9350e+05
Rg (倒空间) rg_reciprocal	23.35 Å
I(0) (倒空间) i0_reciprocal	51750000.0000
解质量估计 total_estimate	0.7971
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	27.4 Å
偏度 Skewness skewness	0.335
峰度 Kurtosis kurtosis	-0.213
角度范围 angular_range	— – 0.3400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	13060000.0000
实空间数据点数 n_real_points	66
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.791; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; 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 (4)

Entity 1 polymer

描述 description	CHONDROITINASE B
分子量 formula_weight	53688.8 kDa
EC 编号 ec_number	4.2.2.4
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	4725

QVVASNETLYQVVKEVKPGGLVQIADGTYKDVQLIVSNSGKSGLPITIKALNPGKVFFTGDAKVELRGEHLILEGIWFKDGNRAIQAWKSHGPGLVAIYGSYNRITACVFDCFDEANSAYITTSLTEDGKVPQHCRIDHCSFTDKITFDQVINLNNTARAIKDGSVGGPAMYHRVDHCFFSNPQKPGNAGGGIRIGYYRNDIGRCLVDSNLFMRQDSEAEIITSKSQENVYYGNTYLNCQGTMNFRHGDHQVAINNFYIGNDQRFGYGGMFVWGSRHVIACNYFELSETIKSRGNAALYLNPGAMASEHALAFDMLIANNAFINVNGYAIHFNPLDERRKEYCAANRLKFETPHQLMLKGNLFFKDKPYVYPFFKDDYFIAGKNSWTGNVALGVEKGIPVNISANRSAYKPVKIKDIQPIEGIALDLNALISKGITGKPLSWDEVRPYWLKEMPGTYALTARLSADRAAKFKAVIKRNKEH

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	;alpha-D-galactopyranose-(1-3)-[beta-D-glucopyranose-(1-4)]2-O-methyl-alpha-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	1119.0 kDa
来源方法 src_method	man
拷贝数 entity_count	1

Entity 3 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-4-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 4 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	806

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6. 折叠分类 (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d1ofma_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.80 — Single-stranded right-handed beta-helix
超家族 Superfamily superfamily	b.80.1 — Pectin lyase-like
家族 Family family	b.80.1.4 — Chondroitinase B

CATH v4.4 (1 domains)

结构域编号 domain_id	1ofmA00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	160 — 3 Solenoid
拓扑 Topology topology	20 — Pectate Lyase C-like
同源超家族 H-superfamily homologous superfamily	10 — Single-stranded right-handed beta-helix, Pectin lyase-like

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7. 引用文献 (1)

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晶胞边长 a length_a	50.537 Å
晶胞边长 b length_b	74.069 Å
晶胞边长 c length_c	58.989 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	93.76 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	2

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	1.800 Å
最低分辨率 resolution_low	33.180 Å
R 因子 r_factor	0.1420
R_work r_work	0.1420
R_free r_free	0.1830

fit	/app/data/saxs_computation/of/1ofm/1ofm.fit
pddf	/app/data/pr_computation/of/1ofm/1ofm.pr.out
profile	/app/data/saxs_computation/of/1ofm/1ofm.dat