SAXSdb — 1ne7

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1ne7
沉积日期 deposition_date	2002-12-10
结构标题 title	;HUMAN GLUCOSAMINE-6-PHOSPHATE DEAMINASE ISOMERASE AT 1.75 A RESOLUTION COMPLEXED WITH N-ACETYL-GLUCOSAMINE-6-PHOSPHATE AND 2-DEOXY-2-AMINO-GLUCITOL-6-PHOSPHATE ;
关键词 keywords	V-TYPE LIKE ALLOSTERIC ENZYME, CONFORMATIONAL DISORDER, CONFORMATIONAL DIFFERENCES, HYDROLASE; 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	36.11 Å
回转半径 Rg (电子) rg_electron	35.25 Å
零角强度 I(0) i0	526930000.00
分子量 molecular_weight	191810.0 kDa
排除体积 excluded_volume	241780 Å³
包络体积 envelope_volume	289340 Å³
水化壳体积 shell_volume	64676 Å³
包络直径 envelope_diameter	121.0 Å
壳层 Rg shell_rg	44.37 Å
包络 Rg envelope_rg	35.42 Å
形状 Rg shape_rg	35.32 Å
总 Rg total_rg	35.59 Å
总原子数 total_atoms	13492
残基数 n_residues	1651
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	110.6 Å
Rg (实空间) rg_real	35.86 Å
Rg 误差 (实空间) rg_real_error	0.64 Å
I(0) (实空间) i0_real	5.2690e+08
I(0) 误差 (实空间) i0_real_error	8.1600e+06
Rg (倒空间) rg_reciprocal	36.02 Å
I(0) (倒空间) i0_reciprocal	527000000.0000
解质量估计 total_estimate	0.8910
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	50.3 Å
偏度 Skewness skewness	0.103
峰度 Kurtosis kurtosis	-0.446
角度范围 angular_range	— – 0.2200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	327400000.0000
实空间数据点数 n_real_points	45
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.909; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.879

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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	Glucosamine-6-phosphate isomerase
分子量 formula_weight	32712.5 kDa
EC 编号 ec_number	3.5.99.6
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	16013

MKLIILEHYSQASEWAAKYIRNRIIQFNPGPEKYFTLGLPTGSTPLGCYKKLIEYYKNGDLSFKYVKTFNMDEYVGLPRDHPESYHSFMWNNFFKHIDIHPENTHILDGNAVDLQAECDAFEEKIKAAGGIELFVGGIGPDGHIAFNEPGSSLVSRTRVKTLAMDTILANARFFDGELTKVPTMALTVGVGTVMDAREVMILITGAHKAFALYKAIEEGVNHMWTVSAFQQHPRTVFVCDEDATLELKVKTVKYFKGLMLVHNKLVDPLYSIKEKETEKSQSSKKPYSD

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 branched

描述 description	alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose
分子量 formula_weight	342.3 kDa
来源方法 src_method	man
拷贝数 entity_count	6

Entity 3 non-polymer

描述 description	2-acetamido-2-deoxy-6-O-phosphono-alpha-D-glucopyranose
分子量 formula_weight	301.2 kDa
来源方法 src_method	man
拷贝数 entity_count	6

Entity 4 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	7

Entity 5 non-polymer

描述 description	2-DEOXY-2-AMINO GLUCITOL-6-PHOSPHATE
分子量 formula_weight	261.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

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	2194

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6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1ne7a_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.124 — NagB/RpiA/CoA transferase-like
超家族 Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
家族 Family family	c.124.1.1 — NagB-like

结构域编号 domain_id	d1ne7b_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.124 — NagB/RpiA/CoA transferase-like
超家族 Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
家族 Family family	c.124.1.1 — NagB-like

结构域编号 domain_id	d1ne7c_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.124 — NagB/RpiA/CoA transferase-like
超家族 Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
家族 Family family	c.124.1.1 — NagB-like

结构域编号 domain_id	d1ne7d_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.124 — NagB/RpiA/CoA transferase-like
超家族 Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
家族 Family family	c.124.1.1 — NagB-like

结构域编号 domain_id	d1ne7e_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.124 — NagB/RpiA/CoA transferase-like
超家族 Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
家族 Family family	c.124.1.1 — NagB-like

结构域编号 domain_id	d1ne7f_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.124 — NagB/RpiA/CoA transferase-like
超家族 Superfamily superfamily	c.124.1 — NagB/RpiA/CoA transferase-like
家族 Family family	c.124.1.1 — NagB-like

CATH v4.4 (6 domains)

结构域编号 domain_id	1ne7A00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1360 —

结构域编号 domain_id	1ne7B00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1360 —

结构域编号 domain_id	1ne7C00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1360 —

结构域编号 domain_id	1ne7D00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1360 —

结构域编号 domain_id	1ne7E00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1360 —

结构域编号 domain_id	1ne7F00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1360 —

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7. 引用文献 (3)

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晶胞边长 a length_a	109.877 Å
晶胞边长 b length_b	110.892 Å
晶胞边长 c length_c	180.881 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 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	—

分辨率 resolution	1.750 Å
最低分辨率 resolution_low	19.970 Å
R 因子 r_factor	0.1954
R_work r_work	0.1930
R_free r_free	0.2170

fit	/app/data/saxs_computation/ne/1ne7/1ne7.fit
pddf	/app/data/pr_computation/ne/1ne7/1ne7.pr.out
profile	/app/data/saxs_computation/ne/1ne7/1ne7.dat

;HUMAN GLUCOSAMINE-6-PHOSPHATE DEAMINASE ISOMERASE AT 1.75 A RESOLUTION COMPLEXED WITH N-ACETYL-GLUCOSAMINE-6-PHOSPHATE AND 2-DEOXY-2-AMINO-GLUCITOL-6-PHOSPHATE ;

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution