1jof

Neurospora crassa 3-carboxy-cis,cis-mucoante lactonizing enzyme

Method: X-RAY DIFFRACTION D_max: 163.6 Å Quality: REASONABLE

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	1jof
沉积日期 deposition_date	2001-07-28
结构标题 title	Neurospora crassa 3-carboxy-cis,cis-mucoante lactonizing enzyme
关键词 keywords	BETA-PROPELLER, HOMOTETRAMER, SEMET-PROTEIN, ISOMERASE; ISOMERASE
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	48.83 Å
回转半径 Rg (电子) rg_electron	48.64 Å
零角强度 I(0) i0	1640760000.00
分子量 molecular_weight	331520.0 kDa
排除体积 excluded_volume	409830 Å³
包络体积 envelope_volume	523700 Å³
水化壳体积 shell_volume	90083 Å³
包络直径 envelope_diameter	165.9 Å
壳层 Rg shell_rg	52.22 Å
包络 Rg envelope_rg	47.82 Å
形状 Rg shape_rg	48.67 Å
总 Rg total_rg	48.67 Å
总原子数 total_atoms	23124
残基数 n_residues	2840
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	163.6 Å
Rg (实空间) rg_real	48.79 Å
Rg 误差 (实空间) rg_real_error	1.31 Å
I(0) (实空间) i0_real	1.6410e+09
I(0) 误差 (实空间) i0_real_error	3.0410e+07
Rg (倒空间) rg_reciprocal	48.83 Å
I(0) (倒空间) i0_reciprocal	1641000000.0000
解质量估计 total_estimate	0.6450
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	61.4 Å
偏度 Skewness skewness	0.314
峰度 Kurtosis kurtosis	-0.388
角度范围 angular_range	— – 0.1600 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	135000000.0000
实空间数据点数 n_real_points	33
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.816; Stabil: 1.000; Sysdev: 0.013; Positv: 1.000; Valcen: 1.000; Smooth: 0.893

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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	CARBOXY-CIS,CIS-MUCONATE CYCLASE
分子量 formula_weight	41715.4 kDa
EC 编号 ec_number	5.5.1.5
来源方法 src_method	man
拷贝数 entity_count	8

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H
原子数 atom_count	23837

PLHHLMIGTWTPPGAIFTVQFDDEKLTCKLIKRTEIPQDEPISWMTFDHERKNIYGAAMKKWSSFAVKSPTEIVHEASHPIGGHPRANDADTNTRAIFLLAAKQPPYAVYANPFYKFAGYGNVFSVSETGKLEKNVQNYEYQENTGIHGMVFDPTETYLYSADLTANKLWTHRKLASGEVELVGSVDAPDPGDHPRWVAMHPTGNYLYALMEAGNRICEYVIDPATHMPVYTHHSFPLIPPGIPDRDPETGKGLYRADVCALTFSGKYMFASSRANKFELQGYIAGFKLRDCGSIEKQLFLSPTPTSGGHSNAVSPCPWSDEWMAITDDQEGWLEIYRWKDEFLHRVARVRIPEPGFGMNAIWYD

来源 Source

来源生物 organism	Neurospora crassa
NCBI 分类编号 ncbi_taxonomy_id	5141
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

Entity 3 non-polymer

描述 description	BETA-MERCAPTOETHANOL
分子量 formula_weight	78.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	16

Entity 4 non-polymer

描述 description	;PIPERAZINE-N,N'-BIS(2-ETHANESULFONIC ACID) ;
分子量 formula_weight	302.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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	713

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1jofa_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.69 — 7-bladed beta-propeller
超家族 Superfamily superfamily	b.69.10 — 3-carboxy-cis,cis-mucoante lactonizing enzyme
家族 Family family	b.69.10.1 — 3-carboxy-cis,cis-mucoante lactonizing enzyme

结构域编号 domain_id	d1jofb_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.69 — 7-bladed beta-propeller
超家族 Superfamily superfamily	b.69.10 — 3-carboxy-cis,cis-mucoante lactonizing enzyme
家族 Family family	b.69.10.1 — 3-carboxy-cis,cis-mucoante lactonizing enzyme

结构域编号 domain_id	d1jofc_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.69 — 7-bladed beta-propeller
超家族 Superfamily superfamily	b.69.10 — 3-carboxy-cis,cis-mucoante lactonizing enzyme
家族 Family family	b.69.10.1 — 3-carboxy-cis,cis-mucoante lactonizing enzyme

结构域编号 domain_id	d1jofd_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.69 — 7-bladed beta-propeller
超家族 Superfamily superfamily	b.69.10 — 3-carboxy-cis,cis-mucoante lactonizing enzyme
家族 Family family	b.69.10.1 — 3-carboxy-cis,cis-mucoante lactonizing enzyme

结构域编号 domain_id	d1jofe_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.69 — 7-bladed beta-propeller
超家族 Superfamily superfamily	b.69.10 — 3-carboxy-cis,cis-mucoante lactonizing enzyme
家族 Family family	b.69.10.1 — 3-carboxy-cis,cis-mucoante lactonizing enzyme

结构域编号 domain_id	d1joff_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.69 — 7-bladed beta-propeller
超家族 Superfamily superfamily	b.69.10 — 3-carboxy-cis,cis-mucoante lactonizing enzyme
家族 Family family	b.69.10.1 — 3-carboxy-cis,cis-mucoante lactonizing enzyme

结构域编号 domain_id	d1jofg_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.69 — 7-bladed beta-propeller
超家族 Superfamily superfamily	b.69.10 — 3-carboxy-cis,cis-mucoante lactonizing enzyme
家族 Family family	b.69.10.1 — 3-carboxy-cis,cis-mucoante lactonizing enzyme

结构域编号 domain_id	d1jofh_
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.69 — 7-bladed beta-propeller
超家族 Superfamily superfamily	b.69.10 — 3-carboxy-cis,cis-mucoante lactonizing enzyme
家族 Family family	b.69.10.1 — 3-carboxy-cis,cis-mucoante lactonizing enzyme

CATH v4.4 (8 domains)

结构域编号 domain_id	1jofA00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	130 — 7 Propeller
拓扑 Topology topology	10 — Methylamine Dehydrogenase; Chain H
同源超家族 H-superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

结构域编号 domain_id	1jofB00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	130 — 7 Propeller
拓扑 Topology topology	10 — Methylamine Dehydrogenase; Chain H
同源超家族 H-superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

结构域编号 domain_id	1jofC00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	130 — 7 Propeller
拓扑 Topology topology	10 — Methylamine Dehydrogenase; Chain H
同源超家族 H-superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

结构域编号 domain_id	1jofD00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	130 — 7 Propeller
拓扑 Topology topology	10 — Methylamine Dehydrogenase; Chain H
同源超家族 H-superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

结构域编号 domain_id	1jofE00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	130 — 7 Propeller
拓扑 Topology topology	10 — Methylamine Dehydrogenase; Chain H
同源超家族 H-superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

结构域编号 domain_id	1jofF00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	130 — 7 Propeller
拓扑 Topology topology	10 — Methylamine Dehydrogenase; Chain H
同源超家族 H-superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

结构域编号 domain_id	1jofG00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	130 — 7 Propeller
拓扑 Topology topology	10 — Methylamine Dehydrogenase; Chain H
同源超家族 H-superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

结构域编号 domain_id	1jofH00
类 Class class	2 — Mainly Beta
架构 Architecture architecture	130 — 7 Propeller
拓扑 Topology topology	10 — Methylamine Dehydrogenase; Chain H
同源超家族 H-superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

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7. 引用文献 (2)

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晶胞边长 a length_a	92.290 Å
晶胞边长 b length_b	160.600 Å
晶胞边长 c length_c	237.500 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	32

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	2.500 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	—
R_work r_work	0.2120
R_free r_free	0.2510

fit	/app/data/saxs_computation/jo/1jof/1jof.fit
pddf	/app/data/pr_computation/jo/1jof/1jof.pr.out
profile	/app/data/saxs_computation/jo/1jof/1jof.dat