1jxa

GLUCOSAMINE 6-PHOSPHATE SYNTHASE WITH GLUCOSE 6-PHOSPHATE

Method: X-RAY DIFFRACTION D_max: 151.4 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	1jxa
沉积日期 deposition_date	2001-09-06
结构标题 title	GLUCOSAMINE 6-PHOSPHATE SYNTHASE WITH GLUCOSE 6-PHOSPHATE
关键词 keywords	beta-sandwich, nucleotide-binding fold, gene duplication, ammonia channel, TRANSFERASE; TRANSFERASE
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	45.83 Å
回转半径 Rg (电子) rg_electron	45.47 Å
零角强度 I(0) i0	594338000.00
分子量 molecular_weight	200660.0 kDa
排除体积 excluded_volume	250960 Å³
包络体积 envelope_volume	323520 Å³
水化壳体积 shell_volume	59341 Å³
包络直径 envelope_diameter	148.9 Å
壳层 Rg shell_rg	49.77 Å
包络 Rg envelope_rg	44.85 Å
形状 Rg shape_rg	45.46 Å
总 Rg total_rg	45.66 Å
总原子数 total_atoms	14117
残基数 n_residues	1824
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	151.4 Å
Rg (实空间) rg_real	45.87 Å
Rg 误差 (实空间) rg_real_error	1.68 Å
I(0) (实空间) i0_real	5.9430e+08
I(0) 误差 (实空间) i0_real_error	1.1140e+07
Rg (倒空间) rg_reciprocal	45.83 Å
I(0) (倒空间) i0_reciprocal	594300000.0000
解质量估计 total_estimate	0.8833
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	40.1 Å
偏度 Skewness skewness	0.222
峰度 Kurtosis kurtosis	-0.781
角度范围 angular_range	— – 0.1700 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	77930000.0000
实空间数据点数 n_real_points	35
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.879; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.867

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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 (3)

Entity 1 polymer

描述 description	glucosamine 6-phosphate synthase
分子量 formula_weight	66818.0 kDa
EC 编号 ec_number	2.6.1.16
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C
原子数 atom_count	14156

CGIVGAIAQRDVAEILLEGLRRLEYRGYDSAGLAVVDAEGHMTRLRRLGKVQMLAQAAEEHPLHGGTGIAHTRWATHGEPSEVNAHPHVSEHIVVVHNGIIENHEPLREELKARGYTFVSETDTEVIAHLVNWELKQGGTLREAVLRAIPQLRGAYGTVIMDSRHPDTLLAARSGSPLVIGLGMGENFIASDQLALLPVTRRFIFLEEGDIAEITRRSVNIFDKTGAEVKRQDIESNLQYDAGDKGIYRHYMQKEIYEQPNAIKNTLTGRISHGQVDLSELGPNADELLSKVEHIQILACGTSYNSGMVSRYWFESLAGIPCDVEIASEFRYRKSAVRRNSLMITLSQSGETADTLAGLRLSKELGYLGSLAICNVPGSSLVRESDLALMTNAGTEIGVASTKAFTTQLTVLLMLVAKLSKLKGLDASIEHDIVHGLQALPSRIEQMLSQDKRIEALAEDFSDKHHALFLGRGDQYPIALEGALKLKEISYIHAEAYAAGELKHGPLALIDADMPVIVVAPNNELLEKLKSNIEEVRARGGQLYVFADQDAGFVSSDNMHIIEMPHVEEVIAPIFYTVPLQLLAYHVALIKGTDVDQPRNLAKSVTVE

来源 Source

来源生物 organism	Escherichia coli
NCBI 分类编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	GLUCOSE-6-PHOSPHATE
分子量 formula_weight	260.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 3 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	39

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6. 折叠分类 (SCOP + CATH) 15 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1jxaa1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.80 — SIS domain
超家族 Superfamily superfamily	c.80.1 — SIS domain
家族 Family family	c.80.1.1 — double-SIS domain

结构域编号 domain_id	d1jxaa2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.153 — Ntn hydrolase-like
超家族 Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family family	d.153.1.1 — Class II glutamine amidotransferases

结构域编号 domain_id	d1jxab1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.80 — SIS domain
超家族 Superfamily superfamily	c.80.1 — SIS domain
家族 Family family	c.80.1.1 — double-SIS domain

结构域编号 domain_id	d1jxab2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.153 — Ntn hydrolase-like
超家族 Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family family	d.153.1.1 — Class II glutamine amidotransferases

结构域编号 domain_id	d1jxac1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.80 — SIS domain
超家族 Superfamily superfamily	c.80.1 — SIS domain
家族 Family family	c.80.1.1 — double-SIS domain

结构域编号 domain_id	d1jxac2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.153 — Ntn hydrolase-like
超家族 Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
家族 Family family	d.153.1.1 — Class II glutamine amidotransferases

CATH v4.4 (9 domains)

结构域编号 domain_id	1jxaA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

结构域编号 domain_id	1jxaA02
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	10490 — Glucose-6-phosphate isomerase like protein; domain 1

结构域编号 domain_id	1jxaA03
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	10490 — Glucose-6-phosphate isomerase like protein; domain 1

结构域编号 domain_id	1jxaB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

结构域编号 domain_id	1jxaB02
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	10490 — Glucose-6-phosphate isomerase like protein; domain 1

结构域编号 domain_id	1jxaB03
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	10490 — Glucose-6-phosphate isomerase like protein; domain 1

结构域编号 domain_id	1jxaC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

结构域编号 domain_id	1jxaC02
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	10490 — Glucose-6-phosphate isomerase like protein; domain 1

结构域编号 domain_id	1jxaC03
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	10490 — Glucose-6-phosphate isomerase like protein; domain 1

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7. 引用文献 (1)

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晶胞边长 a length_a	131.400 Å
晶胞边长 b length_b	112.400 Å
晶胞边长 c length_c	185.100 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	96.40 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	12

空间群 space_group	C 1 2 1
空间群编号 int_tables_number	5
晶系 crystal_system	—

分辨率 resolution	3.100 Å
最低分辨率 resolution_low	12.000 Å
R 因子 r_factor	0.2200
R_work r_work	0.2000
R_free r_free	0.2800

fit	/app/data/saxs_computation/jx/1jxa/1jxa.fit
pddf	/app/data/pr_computation/jx/1jxa/1jxa.pr.out
profile	/app/data/saxs_computation/jx/1jxa/1jxa.dat