1xdo

Crystal Structure of Escherichia coli Polyphosphate Kinase

Method: X-RAY DIFFRACTION D_max: 121.6 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	1xdo
沉积日期 deposition_date	2004-09-07
结构标题 title	Crystal Structure of Escherichia coli Polyphosphate Kinase
关键词 keywords	polyphosphate kinase, PPK, E.coli polyphosphate kinase, 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	38.04 Å
回转半径 Rg (电子) rg_electron	37.05 Å
零角强度 I(0) i0	383277000.00
分子量 molecular_weight	158990.0 kDa
排除体积 excluded_volume	199130 Å³
包络体积 envelope_volume	268590 Å³
水化壳体积 shell_volume	59052 Å³
包络直径 envelope_diameter	130.7 Å
壳层 Rg shell_rg	44.98 Å
包络 Rg envelope_rg	35.83 Å
形状 Rg shape_rg	37.03 Å
总 Rg total_rg	37.65 Å
总原子数 total_atoms	11234
残基数 n_residues	1374
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	121.6 Å
Rg (实空间) rg_real	37.88 Å
Rg 误差 (实空间) rg_real_error	0.91 Å
I(0) (实空间) i0_real	3.8330e+08
I(0) 误差 (实空间) i0_real_error	5.4900e+06
Rg (倒空间) rg_reciprocal	37.99 Å
I(0) (倒空间) i0_reciprocal	383300000.0000
解质量估计 total_estimate	0.8961
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	49.2 Å
偏度 Skewness skewness	0.186
峰度 Kurtosis kurtosis	-0.463
角度范围 angular_range	— – 0.2100 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	109800000.0000
实空间数据点数 n_real_points	43
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.918; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.900

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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 (1)

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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	d1xdoa1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.7 — Spectrin repeat-like
超家族 Superfamily superfamily	a.7.15 — PPK N-terminal domain-like
家族 Family family	a.7.15.1 — PPK N-terminal domain-like

结构域编号 domain_id	d1xdoa2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.322 — PHP14-like
超家族 Superfamily superfamily	d.322.1 — PHP14-like
家族 Family family	d.322.1.2 — PPK middle domain-like

结构域编号 domain_id	d1xdoa3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.136 — Phospholipase D/nuclease
超家族 Superfamily superfamily	d.136.1 — Phospholipase D/nuclease
家族 Family family	d.136.1.4 — Polyphosphate kinase C-terminal domain

结构域编号 domain_id	d1xdoa4
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.136 — Phospholipase D/nuclease
超家族 Superfamily superfamily	d.136.1 — Phospholipase D/nuclease
家族 Family family	d.136.1.4 — Polyphosphate kinase C-terminal domain

结构域编号 domain_id	d1xdob1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.7 — Spectrin repeat-like
超家族 Superfamily superfamily	a.7.15 — PPK N-terminal domain-like
家族 Family family	a.7.15.1 — PPK N-terminal domain-like

结构域编号 domain_id	d1xdob2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.322 — PHP14-like
超家族 Superfamily superfamily	d.322.1 — PHP14-like
家族 Family family	d.322.1.2 — PPK middle domain-like

结构域编号 domain_id	d1xdob3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.136 — Phospholipase D/nuclease
超家族 Superfamily superfamily	d.136.1 — Phospholipase D/nuclease
家族 Family family	d.136.1.4 — Polyphosphate kinase C-terminal domain

结构域编号 domain_id	d1xdob4
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.136 — Phospholipase D/nuclease
超家族 Superfamily superfamily	d.136.1 — Phospholipase D/nuclease
家族 Family family	d.136.1.4 — Polyphosphate kinase C-terminal domain

CATH v4.4 (8 domains)

结构域编号 domain_id	1xdoA01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily	310 — Polyphosphate kinase N-terminal domain

结构域编号 domain_id	1xdoA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1840 — polyphosphate kinase like
同源超家族 H-superfamily homologous superfamily	10 — Polyphosphate kinase middle domain

结构域编号 domain_id	1xdoA03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	870 — Endonuclease; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Endonuclease Chain A

结构域编号 domain_id	1xdoA04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	870 — Endonuclease; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Endonuclease Chain A

结构域编号 domain_id	1xdoB01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
同源超家族 H-superfamily homologous superfamily	310 — Polyphosphate kinase N-terminal domain

结构域编号 domain_id	1xdoB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1840 — polyphosphate kinase like
同源超家族 H-superfamily homologous superfamily	10 — Polyphosphate kinase middle domain

结构域编号 domain_id	1xdoB03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	870 — Endonuclease; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Endonuclease Chain A

结构域编号 domain_id	1xdoB04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	870 — Endonuclease; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Endonuclease Chain A

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7. 引用文献 (1)

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晶胞边长 a length_a	154.000 Å
晶胞边长 b length_b	154.000 Å
晶胞边长 c length_c	155.000 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	16

空间群 space_group	P 42 21 2
空间群编号 int_tables_number	94
晶系 crystal_system	—

分辨率 resolution	3.000 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	0.2650
R_work r_work	0.2550
R_free r_free	0.2730

描述 description	Polyphosphate kinase
分子量 formula_weight	80414.2 kDa
EC 编号 ec_number	2.7.4.1
来源方法 src_method	man
拷贝数 entity_count	2

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	11234

Crystal Structure of Escherichia coli Polyphosphate Kinase

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

4. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

5. 实体与聚合体信息 (1)

Entity 1 polymer

聚合体 Polymer

来源 Source

6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)

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

fit	/app/data/saxs_computation/xd/1xdo/1xdo.fit
pddf	/app/data/pr_computation/xd/1xdo/1xdo.pr.out
profile	/app/data/saxs_computation/xd/1xdo/1xdo.dat