2jkb

Crystal structure of Streptococcus pneumoniae NanB in complex with 2, 7-anhydro-Neu5Ac

Method: X-RAY DIFFRACTION D_max: 92.7 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	2jkb
沉积日期 deposition_date	2008-08-26
结构标题 title	Crystal structure of Streptococcus pneumoniae NanB in complex with 2, 7-anhydro-Neu5Ac
关键词 keywords	INTRAMOLECULAR TRANS-SIALIDASE, LYASE, GLYCOSIDASE, NEURAMINIDASE; 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	27.98 Å
回转半径 Rg (电子) rg_electron	27.24 Å
零角强度 I(0) i0	89525700.00
分子量 molecular_weight	74485.0 kDa
排除体积 excluded_volume	93134 Å³
包络体积 envelope_volume	109490 Å³
水化壳体积 shell_volume	33654 Å³
包络直径 envelope_diameter	96.4 Å
壳层 Rg shell_rg	34.50 Å
包络 Rg envelope_rg	27.59 Å
形状 Rg shape_rg	27.21 Å
总 Rg total_rg	28.04 Å
总原子数 total_atoms	5257
残基数 n_residues	661
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	92.7 Å
Rg (实空间) rg_real	28.01 Å
Rg 误差 (实空间) rg_real_error	0.71 Å
I(0) (实空间) i0_real	8.9530e+07
I(0) 误差 (实空间) i0_real_error	1.5280e+06
Rg (倒空间) rg_reciprocal	28.00 Å
I(0) (倒空间) i0_reciprocal	89530000.0000
解质量估计 total_estimate	0.8826
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	30.9 Å
偏度 Skewness skewness	0.396
峰度 Kurtosis kurtosis	-0.323
角度范围 angular_range	— – 0.2850 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	20040000.0000
实空间数据点数 n_real_points	58
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.843; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.950

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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	SIALIDASE B
分子量 formula_weight	76741.3 kDa
EC 编号 ec_number	4.2.2.15
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	6507

AHHHHHHSSGLEVLFQGPNELNYGQLSISPIFQGGSYQLNNKSIDISSLLLDKLSGESQTVVMKFKADKPNSLQALFGLSNSKAGFKNNYFSIFMRDSGEIGVEIRDAQKGINYLFSRPASLWGKHKGQAVENTLVFVSDSKDKTYTMYVNGIEVFSETVDTFLPISNINGIDKATLGAVNREGKEHYLAKGSIDEISLFNKAISDQEVSTIPLSNPFQLIFQSGDSTQANYFRIPTLYTLSSGRVLSSIDARYGGTHDSKSKINIATSYSDDNGKTWSEPIFAMKFNDYEEQLVYWPRDNKLKNSQISGSASFIDSSIVEDKKSGKTILLADVMPAGIGNNNANKADSGFKEINGHYYLKLKKNGDNDFRYTVRENGVVYNETTNKPTNYTINDKYEVLEGGKSLTVEQYSVDFDSGSLRERHNGKQVPMNVFYKDSLFKVTPTNYIAMTTSQNRGESWEQFKLLPPFLGEKHNGTYLCPGQGLALKSSNRLIFATYTSGELTYLISDDSGQTWKKSSASIPFKNATAEAQMVELRDGVIRTFFRTTTGKIAYMTSRDSGETWSKVSYIDGIQQTSYGTQVSAIKYSQLIDGKEAVILSTPNSRSGRKGGQLVVGLVNKEDDSIDWKYHYDIDLPSYGYAYSAITELPNHHIGVLFEKYDSWSRNELHLSNVVQYIDLEINDLTK

来源 Source

来源生物 organism	STREPTOCOCCUS PNEUMONIAE
NCBI 分类编号 ncbi_taxonomy_id	170187
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 non-polymer

描述 description	2-ACETYLAMINO-7-(1,2-DIHYDROXY-ETHYL)-3-HYDROXY-6,8-DIOXA-BICYCLO[3.2.1]OCTANE-5-CARBOXYLIC ACID
分子量 formula_weight	291.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 non-polymer

描述 description	1,2-ETHANEDIOL
分子量 formula_weight	62.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

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	1024

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6. 折叠分类 (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

结构域编号 domain_id	2jkbA01
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	200 —

结构域编号 domain_id	2jkbA02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	120 — 6 Propeller
拓扑 Topology topology	10 — Neuraminidase
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	2jkbA03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	220 — Intramolecular trans-sialidase; domain 3
同源超家族 H-superfamily homologous superfamily	10 — Intramolecular Trans-sialidase; Domain 3

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7. 引用文献 (1)

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晶胞边长 a length_a	76.719 Å
晶胞边长 b length_b	82.746 Å
晶胞边长 c length_c	118.079 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	4

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	1.540 Å
最低分辨率 resolution_low	23.930 Å
R 因子 r_factor	0.1630
R_work r_work	0.1620
R_free r_free	0.1880

fit	/app/data/saxs_computation/jk/2jkb/2jkb.fit
pddf	/app/data/pr_computation/jk/2jkb/2jkb.pr.out
profile	/app/data/saxs_computation/jk/2jkb/2jkb.dat