1zxy

Anthranilate Phosphoribosyltransferase from Sulfolobus solfataricus in complex with PRPP and Magnesium

Method: X-RAY DIFFRACTION D_max: 143.5 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	1zxy
沉积日期 deposition_date	2005-06-09
结构标题 title	Anthranilate Phosphoribosyltransferase from Sulfolobus solfataricus in complex with PRPP and Magnesium
关键词 keywords	Anthranilate Posphoribosyltransferase, TrpD, PRPP, 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	48.82 Å
回转半径 Rg (电子) rg_electron	48.37 Å
零角强度 I(0) i0	308507000.00
分子量 molecular_weight	151750.0 kDa
排除体积 excluded_volume	192510 Å³
包络体积 envelope_volume	268500 Å³
水化壳体积 shell_volume	45090 Å³
包络直径 envelope_diameter	151.1 Å
壳层 Rg shell_rg	56.43 Å
包络 Rg envelope_rg	45.64 Å
形状 Rg shape_rg	48.39 Å
总 Rg total_rg	48.56 Å
总原子数 total_atoms	10656
残基数 n_residues	1376
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	143.5 Å
Rg (实空间) rg_real	48.64 Å
Rg 误差 (实空间) rg_real_error	1.26 Å
I(0) (实空间) i0_real	3.0850e+08
I(0) 误差 (实空间) i0_real_error	5.8820e+06
Rg (倒空间) rg_reciprocal	48.82 Å
I(0) (倒空间) i0_reciprocal	308600000.0000
解质量估计 total_estimate	0.7628
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	76.2 Å
偏度 Skewness skewness	-0.103
峰度 Kurtosis kurtosis	-0.887
角度范围 angular_range	— – 0.1600 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	11070000.0000
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: 0.539; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.938; Smooth: 0.358

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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	Anthranilate phosphoribosyltransferase
分子量 formula_weight	37619.5 kDa
EC 编号 ec_number	2.4.2.18
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	10748

MNINEILKKLINKSDLEINEAEELAKAIIRGEVPEILVSAILVALRMKGESKNEIVGFARAMRELAIKIDVPNAIDTAGTGGDGLGTVNVSTASAILLSLVNPVAKHGNRAVSGKSGSADVLEALGYNIIVPPERAKELVNKTNFVFLFAQYYHPAMKNVANVRKTLGIRTIFNILGPLTNPANAKYQLMGVFSKDHLDLLSKSAYELDFNKIILVYGEPGIDEVSPIGNTFMKIVSKRGIEEVKLNVTDFGISPIPIEKLIVNSAEDSAIKIVRAFLGKDEHVAEFIKINTAVALFALDRVGDFREGYEYADHLIEKSLDKLNEIISMNGDVTKLKTIVVKSSG

来源 Source

来源生物 organism	Sulfolobus solfataricus
NCBI 分类编号 ncbi_taxonomy_id	2287
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	8

Entity 3 non-polymer

描述 description	1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose
分子量 formula_weight	390.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

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	92

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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	d1zxya1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.46 — Methionine synthase domain-like
超家族 Superfamily superfamily	a.46.2 — Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain
家族 Family family	a.46.2.1 — Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain

结构域编号 domain_id	d1zxya2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.27 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain
超家族 Superfamily superfamily	c.27.1 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain
家族 Family family	c.27.1.1 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain

结构域编号 domain_id	d1zxyb1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.46 — Methionine synthase domain-like
超家族 Superfamily superfamily	a.46.2 — Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain
家族 Family family	a.46.2.1 — Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain

结构域编号 domain_id	d1zxyb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.27 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain
超家族 Superfamily superfamily	c.27.1 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain
家族 Family family	c.27.1.1 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain

结构域编号 domain_id	d1zxyc1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.46 — Methionine synthase domain-like
超家族 Superfamily superfamily	a.46.2 — Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain
家族 Family family	a.46.2.1 — Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain

结构域编号 domain_id	d1zxyc2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.27 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain
超家族 Superfamily superfamily	c.27.1 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain
家族 Family family	c.27.1.1 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain

结构域编号 domain_id	d1zxyd1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.46 — Methionine synthase domain-like
超家族 Superfamily superfamily	a.46.2 — Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain
家族 Family family	a.46.2.1 — Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain

结构域编号 domain_id	d1zxyd2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.27 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain
超家族 Superfamily superfamily	c.27.1 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain
家族 Family family	c.27.1.1 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain

CATH v4.4 (8 domains)

结构域编号 domain_id	1zxyA01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	970 — Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C

结构域编号 domain_id	1zxyA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1030 — Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain

结构域编号 domain_id	1zxyB01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	970 — Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C

结构域编号 domain_id	1zxyB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1030 — Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain

结构域编号 domain_id	1zxyC01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	970 — Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C

结构域编号 domain_id	1zxyC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1030 — Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain

结构域编号 domain_id	1zxyD01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	970 — Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3
同源超家族 H-superfamily homologous superfamily	10 — Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C

结构域编号 domain_id	1zxyD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	1030 — Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain

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7. 引用文献 (1)

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晶胞边长 a length_a	92.694 Å
晶胞边长 b length_b	65.806 Å
晶胞边长 c length_c	116.722 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	107.80 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	P 1 2 1
空间群编号 int_tables_number	3
晶系 crystal_system	—

分辨率 resolution	2.560 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	—
R_work r_work	0.2040
R_free r_free	0.2600

fit	/app/data/saxs_computation/zx/1zxy/1zxy.fit
pddf	/app/data/pr_computation/zx/1zxy/1zxy.pr.out
profile	/app/data/saxs_computation/zx/1zxy/1zxy.dat