1v0f

Endosialidase of Bacteriophage K1F in complex with oligomeric alpha-2,8-sialic acid

Method: X-RAY DIFFRACTION D_max: 185.5 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	1v0f
沉积日期 deposition_date	2004-03-28
结构标题 title	Endosialidase of Bacteriophage K1F in complex with oligomeric alpha-2,8-sialic acid
关键词 keywords	ENDOSIALIDASE, POLYSIALIC ACID DEGRADATION, HYDROLASE, GLYCOSIDASE.; HYDROLASE
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	55.36 Å
回转半径 Rg (电子) rg_electron	55.27 Å
零角强度 I(0) i0	3030180000.00
分子量 molecular_weight	448360.0 kDa
排除体积 excluded_volume	553810 Å³
包络体积 envelope_volume	735260 Å³
水化壳体积 shell_volume	108130 Å³
包络直径 envelope_diameter	181.2 Å
壳层 Rg shell_rg	60.31 Å
包络 Rg envelope_rg	54.20 Å
形状 Rg shape_rg	55.27 Å
总 Rg total_rg	55.38 Å
总原子数 total_atoms	31659
残基数 n_residues	3996
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	185.5 Å
Rg (实空间) rg_real	55.41 Å
Rg 误差 (实空间) rg_real_error	1.72 Å
I(0) (实空间) i0_real	3.0300e+09
I(0) 误差 (实空间) i0_real_error	5.3670e+07
Rg (倒空间) rg_reciprocal	55.30 Å
I(0) (倒空间) i0_reciprocal	3030000000.0000
解质量估计 total_estimate	0.8560
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	59.6 Å
偏度 Skewness skewness	0.368
峰度 Kurtosis kurtosis	-0.437
角度范围 angular_range	— – 0.1400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	247300000.0000
实空间数据点数 n_real_points	29
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.853; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.566

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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	ENDO-ALPHA-SIALIDASE
分子量 formula_weight	74132.0 kDa
EC 编号 ec_number	3.2.1.129
来源方法 src_method	man
拷贝数 entity_count	6

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F
原子数 atom_count	32580

SAKGDGVTDDTAALTSALNDTPVGQKINGNGKTYKVTSLPDISRFINTRFVYERIPGQPLYYASEEFVQGELFKITDTPYYNAWPQDKAFVYENVIYAPYMGSDRHGVSRLHVSWVKSGDDGQTWSTPEWLTDLHPDYPTVNYHCMSMGVCRNRLFAMIETRTLAKNALTNCALWDRPMSRSLHLTGGITKAANQRYATIHVPDHGLFVGDFVNFSNSAVTGVSGDMTVATVIDKDNFTVLTPNQQTSDLNNAGKNWHMGTSFHKSPWRKTDLGLIPSVTEVHSFATIDNNGFAMGYHQGDVAPREVGLFYFPDAFNSPSNYVRRQIPSEYEPDASEPCIKYYDGVLYLITRGTRGDRLGSSLHRSRDIGQTWESLRFPHNVHHTTLPFAKVGDDLIMFGSERAENEWEAGAPDDRYKASYPRTFYARLNVNNWNADDIEWVNITDQIYQGGIVNSGVGVGSVVVKDNYIYYMFGGEDHFNPWTYGDNSAKDPFKSDGHPSDLYCYKMKIGPDNRVSRDFRYGAVPNRAVPVFFDTNGVRTVPAPMEFTGDLGLGHVTIRASTSSNIRSEVLMEGEYGFIGKSIPTDNPAGQRIIFCGGEGTSSTTGAQITLYGANNTDSRRIVYNGDEHLFQSADVKPYNDNVTALGGPSNRFTTAYLGSNPIVT

来源 Source

来源生物 organism	COLIPHAGE K1F
NCBI 分类编号 ncbi_taxonomy_id	344021
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 branched

描述 description	N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-alpha-neuraminic acid
分子量 formula_weight	600.5 kDa
来源方法 src_method	man
拷贝数 entity_count	3

Entity 3 non-polymer

描述 description	N-acetyl-beta-neuraminic acid
分子量 formula_weight	309.3 kDa
来源方法 src_method	man
拷贝数 entity_count	6

Entity 4 non-polymer

描述 description	PHOSPHATE ION
分子量 formula_weight	95.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

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	921

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6. 折叠分类 (SCOP + CATH) 36 domains

SCOP 2.08 (12 domains)

结构域编号 domain_id	d1v0fa1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.68 — 6-bladed beta-propeller
超家族 Superfamily superfamily	b.68.1 — Sialidases
家族 Family family	b.68.1.2 — Endo-alpha-sialidase

结构域编号 domain_id	d1v0fa2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.108 — Triple-stranded beta-helix
超家族 Superfamily superfamily	b.108.1 — Phage fibre proteins
家族 Family family	b.108.1.3 — Endo-alpha-sialidase

结构域编号 domain_id	d1v0fb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.68 — 6-bladed beta-propeller
超家族 Superfamily superfamily	b.68.1 — Sialidases
家族 Family family	b.68.1.2 — Endo-alpha-sialidase

结构域编号 domain_id	d1v0fb2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.108 — Triple-stranded beta-helix
超家族 Superfamily superfamily	b.108.1 — Phage fibre proteins
家族 Family family	b.108.1.3 — Endo-alpha-sialidase

结构域编号 domain_id	d1v0fc1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.68 — 6-bladed beta-propeller
超家族 Superfamily superfamily	b.68.1 — Sialidases
家族 Family family	b.68.1.2 — Endo-alpha-sialidase

结构域编号 domain_id	d1v0fc2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.108 — Triple-stranded beta-helix
超家族 Superfamily superfamily	b.108.1 — Phage fibre proteins
家族 Family family	b.108.1.3 — Endo-alpha-sialidase

结构域编号 domain_id	d1v0fd1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.68 — 6-bladed beta-propeller
超家族 Superfamily superfamily	b.68.1 — Sialidases
家族 Family family	b.68.1.2 — Endo-alpha-sialidase

结构域编号 domain_id	d1v0fd2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.108 — Triple-stranded beta-helix
超家族 Superfamily superfamily	b.108.1 — Phage fibre proteins
家族 Family family	b.108.1.3 — Endo-alpha-sialidase

结构域编号 domain_id	d1v0fe1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.68 — 6-bladed beta-propeller
超家族 Superfamily superfamily	b.68.1 — Sialidases
家族 Family family	b.68.1.2 — Endo-alpha-sialidase

结构域编号 domain_id	d1v0fe2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.108 — Triple-stranded beta-helix
超家族 Superfamily superfamily	b.108.1 — Phage fibre proteins
家族 Family family	b.108.1.3 — Endo-alpha-sialidase

结构域编号 domain_id	d1v0ff1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.68 — 6-bladed beta-propeller
超家族 Superfamily superfamily	b.68.1 — Sialidases
家族 Family family	b.68.1.2 — Endo-alpha-sialidase

结构域编号 domain_id	d1v0ff2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.108 — Triple-stranded beta-helix
超家族 Superfamily superfamily	b.108.1 — Phage fibre proteins
家族 Family family	b.108.1.3 — Endo-alpha-sialidase

CATH v4.4 (24 domains)

结构域编号 domain_id	1v0fA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	750 — Transcription Regulator spoIIAA
同源超家族 H-superfamily homologous superfamily	60 — Endosialidase, N-terminal extension domain

结构域编号 domain_id	1v0fA02
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	1v0fA03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1v0fA04
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	1090 — Endosialidase, domain 4
同源超家族 H-superfamily homologous superfamily	10 — Endosialidase, domain 4

结构域编号 domain_id	1v0fB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	750 — Transcription Regulator spoIIAA
同源超家族 H-superfamily homologous superfamily	60 — Endosialidase, N-terminal extension domain

结构域编号 domain_id	1v0fB02
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	1v0fB03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1v0fB04
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	1090 — Endosialidase, domain 4
同源超家族 H-superfamily homologous superfamily	10 — Endosialidase, domain 4

结构域编号 domain_id	1v0fC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	750 — Transcription Regulator spoIIAA
同源超家族 H-superfamily homologous superfamily	60 — Endosialidase, N-terminal extension domain

结构域编号 domain_id	1v0fC02
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	1v0fC03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1v0fC04
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	1090 — Endosialidase, domain 4
同源超家族 H-superfamily homologous superfamily	10 — Endosialidase, domain 4

结构域编号 domain_id	1v0fD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	750 — Transcription Regulator spoIIAA
同源超家族 H-superfamily homologous superfamily	60 — Endosialidase, N-terminal extension domain

结构域编号 domain_id	1v0fD02
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	1v0fD03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1v0fD04
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	1090 — Endosialidase, domain 4
同源超家族 H-superfamily homologous superfamily	10 — Endosialidase, domain 4

结构域编号 domain_id	1v0fE01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	750 — Transcription Regulator spoIIAA
同源超家族 H-superfamily homologous superfamily	60 — Endosialidase, N-terminal extension domain

结构域编号 domain_id	1v0fE02
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	1v0fE03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1v0fE04
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	1090 — Endosialidase, domain 4
同源超家族 H-superfamily homologous superfamily	10 — Endosialidase, domain 4

结构域编号 domain_id	1v0fF01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	750 — Transcription Regulator spoIIAA
同源超家族 H-superfamily homologous superfamily	60 — Endosialidase, N-terminal extension domain

结构域编号 domain_id	1v0fF02
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	1v0fF03
类 Class class	2 — Mainly Beta
架构 Architecture architecture	40 — Beta Barrel
拓扑 Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
同源超家族 H-superfamily homologous superfamily	20 —

结构域编号 domain_id	1v0fF04
类 Class class	4 — Few Secondary Structures
架构 Architecture architecture	10 — Irregular
拓扑 Topology topology	1090 — Endosialidase, domain 4
同源超家族 H-superfamily homologous superfamily	10 — Endosialidase, domain 4

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7. 引用文献 (2)

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晶胞边长 a length_a	99.540 Å
晶胞边长 b length_b	131.400 Å
晶胞边长 c length_c	346.040 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	24

空间群 space_group	P 2 2 21
空间群编号 int_tables_number	17
晶系 crystal_system	—

分辨率 resolution	2.550 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.1826
R_work r_work	0.1800
R_free r_free	0.2315

fit	/app/data/saxs_computation/v0/1v0f/1v0f.fit
pddf	/app/data/pr_computation/v0/1v0f/1v0f.pr.out
profile	/app/data/saxs_computation/v0/1v0f/1v0f.dat