1p0z

Sensor Kinase CitA binding domain

Method: X-RAY DIFFRACTION D_max: 141.8 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	1p0z
沉积日期 deposition_date	2003-04-11
结构标题 title	Sensor Kinase CitA binding domain
关键词 keywords	Transferase, Kinase; 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	45.04 Å
回转半径 Rg (电子) rg_electron	44.89 Å
零角强度 I(0) i0	472838000.00
分子量 molecular_weight	156330.0 kDa
排除体积 excluded_volume	185190 Å³
包络体积 envelope_volume	298030 Å³
水化壳体积 shell_volume	57416 Å³
包络直径 envelope_diameter	152.5 Å
壳层 Rg shell_rg	48.21 Å
包络 Rg envelope_rg	42.67 Å
形状 Rg shape_rg	44.91 Å
总 Rg total_rg	44.98 Å
总原子数 total_atoms	10470
残基数 n_residues	1310
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	141.8 Å
Rg (实空间) rg_real	44.88 Å
Rg 误差 (实空间) rg_real_error	1.04 Å
I(0) (实空间) i0_real	4.7280e+08
I(0) 误差 (实空间) i0_real_error	7.9670e+06
Rg (倒空间) rg_reciprocal	45.04 Å
I(0) (倒空间) i0_reciprocal	472900000.0000
解质量估计 total_estimate	0.8731
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	60.8 Å
偏度 Skewness skewness	0.147
峰度 Kurtosis kurtosis	-0.266
角度范围 angular_range	— – 0.1750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	10420000.0000
实空间数据点数 n_real_points	36
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.873; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.735

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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	Sensor kinase citA
分子量 formula_weight	14315.2 kDa
EC 编号 ec_number	2.7.13.3
来源方法 src_method	man
拷贝数 entity_count	10

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,I,J
原子数 atom_count	12523

EERLHYQVGQRALIQAMQISAMPELVEAVQKRDLARIKALIDPMRSFSDATYITVGDASGQRLYHVNPDEIGKSMEGGDSDEALINAKSYVSVRKGSLGSSLRGKSPIQDATGKVIGIVSVGYTIEQLEHH

来源 Source

来源生物 organism	Klebsiella pneumoniae
NCBI 分类编号 ncbi_taxonomy_id	573
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	CITRATE ANION
分子量 formula_weight	189.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	10

Entity 3 non-polymer

描述 description	SODIUM ION
分子量 formula_weight	23.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	10

Entity 4 non-polymer

描述 description	bis(mu4-oxo)-bis(mu3-oxo)-octakis(mu2-oxo)-dodecaoxo-heptamolybdenum (VI)
分子量 formula_weight	1055.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	10

Entity 5 non-polymer

描述 description	MO(VI)(=O)(OH)2 CLUSTER
分子量 formula_weight	146.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	10

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	1573

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6. 折叠分类 (SCOP + CATH) 30 domains

SCOP 2.08 (20 domains)

结构域编号 domain_id	d1p0za1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.110 — Profilin-like
超家族 Superfamily superfamily	d.110.6 — Sensory domain-like
家族 Family family	d.110.6.1 — Sensory domain of two-component sensor kinase

结构域编号 domain_id	d1p0za2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1p0zb1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.110 — Profilin-like
超家族 Superfamily superfamily	d.110.6 — Sensory domain-like
家族 Family family	d.110.6.1 — Sensory domain of two-component sensor kinase

结构域编号 domain_id	d1p0zb2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1p0zc1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.110 — Profilin-like
超家族 Superfamily superfamily	d.110.6 — Sensory domain-like
家族 Family family	d.110.6.1 — Sensory domain of two-component sensor kinase

结构域编号 domain_id	d1p0zc2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1p0zd1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.110 — Profilin-like
超家族 Superfamily superfamily	d.110.6 — Sensory domain-like
家族 Family family	d.110.6.1 — Sensory domain of two-component sensor kinase

结构域编号 domain_id	d1p0zd2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1p0ze1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.110 — Profilin-like
超家族 Superfamily superfamily	d.110.6 — Sensory domain-like
家族 Family family	d.110.6.1 — Sensory domain of two-component sensor kinase

结构域编号 domain_id	d1p0ze2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1p0zf1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.110 — Profilin-like
超家族 Superfamily superfamily	d.110.6 — Sensory domain-like
家族 Family family	d.110.6.1 — Sensory domain of two-component sensor kinase

结构域编号 domain_id	d1p0zf2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1p0zg1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.110 — Profilin-like
超家族 Superfamily superfamily	d.110.6 — Sensory domain-like
家族 Family family	d.110.6.1 — Sensory domain of two-component sensor kinase

结构域编号 domain_id	d1p0zg2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1p0zh1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.110 — Profilin-like
超家族 Superfamily superfamily	d.110.6 — Sensory domain-like
家族 Family family	d.110.6.1 — Sensory domain of two-component sensor kinase

结构域编号 domain_id	d1p0zh2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1p0zi1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.110 — Profilin-like
超家族 Superfamily superfamily	d.110.6 — Sensory domain-like
家族 Family family	d.110.6.1 — Sensory domain of two-component sensor kinase

结构域编号 domain_id	d1p0zi2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

结构域编号 domain_id	d1p0zj1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.110 — Profilin-like
超家族 Superfamily superfamily	d.110.6 — Sensory domain-like
家族 Family family	d.110.6.1 — Sensory domain of two-component sensor kinase

结构域编号 domain_id	d1p0zj2
类 Class class	l — Artifacts
折叠类型 Fold fold	l.1 — Tags
超家族 Superfamily superfamily	l.1.1 — Tags
家族 Family family	l.1.1.1 — Tags

CATH v4.4 (10 domains)

结构域编号 domain_id	1p0zA00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	450 — Beta-Lactamase
同源超家族 H-superfamily homologous superfamily	20 — PAS domain

结构域编号 domain_id	1p0zB00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	450 — Beta-Lactamase
同源超家族 H-superfamily homologous superfamily	20 — PAS domain

结构域编号 domain_id	1p0zC00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	450 — Beta-Lactamase
同源超家族 H-superfamily homologous superfamily	20 — PAS domain

结构域编号 domain_id	1p0zD00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	450 — Beta-Lactamase
同源超家族 H-superfamily homologous superfamily	20 — PAS domain

结构域编号 domain_id	1p0zE00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	450 — Beta-Lactamase
同源超家族 H-superfamily homologous superfamily	20 — PAS domain

结构域编号 domain_id	1p0zF00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	450 — Beta-Lactamase
同源超家族 H-superfamily homologous superfamily	20 — PAS domain

结构域编号 domain_id	1p0zG00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	450 — Beta-Lactamase
同源超家族 H-superfamily homologous superfamily	20 — PAS domain

结构域编号 domain_id	1p0zH00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	450 — Beta-Lactamase
同源超家族 H-superfamily homologous superfamily	20 — PAS domain

结构域编号 domain_id	1p0zI00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	450 — Beta-Lactamase
同源超家族 H-superfamily homologous superfamily	20 — PAS domain

结构域编号 domain_id	1p0zJ00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	450 — Beta-Lactamase
同源超家族 H-superfamily homologous superfamily	20 — PAS domain

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7. 引用文献 (1)

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晶胞边长 a length_a	61.613 Å
晶胞边长 b length_b	84.333 Å
晶胞边长 c length_c	97.710 Å
晶胞夹角 α angle_alpha	112.83 °
晶胞夹角 β angle_beta	107.36 °
晶胞夹角 γ angle_gamma	93.74 °
晶胞分子数 Z z_pdb	10

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

分辨率 resolution	1.600 Å
最低分辨率 resolution_low	38.030 Å
R 因子 r_factor	0.1680
R_work r_work	0.1680
R_free r_free	0.1900

fit	/app/data/saxs_computation/p0/1p0z/1p0z.fit
pddf	/app/data/pr_computation/p0/1p0z/1p0z.pr.out
profile	/app/data/saxs_computation/p0/1p0z/1p0z.dat