1qz0

Crystal Structure of the Yersinia Pestis Phosphatase YopH in Complex with a Phosphotyrosyl Mimetic-Containing Hexapeptide

Method: X-RAY DIFFRACTION D_max: 107.2 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	1qz0
沉积日期 deposition_date	2003-09-15
结构标题 title	Crystal Structure of the Yersinia Pestis Phosphatase YopH in Complex with a Phosphotyrosyl Mimetic-Containing Hexapeptide
关键词 keywords	PHOSPHATASE, PTPASE, YOPH, DEPHOSPHORYLASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX; HYDROLASE/HYDROLASE INHIBITOR
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	30.16 Å
回转半径 Rg (电子) rg_electron	29.89 Å
零角强度 I(0) i0	77752900.00
分子量 molecular_weight	65015.0 kDa
排除体积 excluded_volume	79651 Å³
包络体积 envelope_volume	98581 Å³
水化壳体积 shell_volume	29004 Å³
包络直径 envelope_diameter	114.4 Å
壳层 Rg shell_rg	34.69 Å
包络 Rg envelope_rg	29.91 Å
形状 Rg shape_rg	29.88 Å
总 Rg total_rg	30.34 Å
总原子数 total_atoms	4534
残基数 n_residues	580
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	107.2 Å
Rg (实空间) rg_real	30.42 Å
Rg 误差 (实空间) rg_real_error	1.14 Å
I(0) (实空间) i0_real	7.7750e+07
I(0) 误差 (实空间) i0_real_error	1.3390e+06
Rg (倒空间) rg_reciprocal	30.31 Å
I(0) (倒空间) i0_reciprocal	77750000.0000
解质量估计 total_estimate	0.8137
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	28.3 Å
偏度 Skewness skewness	0.545
峰度 Kurtosis kurtosis	-0.285
角度范围 angular_range	— – 0.2650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	21240000.0000
实空间数据点数 n_real_points	54
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.629; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.703; Smooth: 0.985

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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	Protein-tyrosine phosphatase yopH
分子量 formula_weight	33553.9 kDa
EC 编号 ec_number	3.1.3.48
突变 mutation	C235R
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	5137

MRERPHTSGHHGAGEARATAPSTVSPYGPEARAELSSRLTTLRNTLAPATNDPRYLQACGGEKLNRFRDIQCRRQTAVRADLNANYIQVGNTRTIACQYPLQSQLESHFRMLAENRTPVLAVLASSSEIANQRFGMPDYFRQSGTYGSITVESKMTQQVGLGDGIMADMYTLTIREAGQKTISVPVVHVGNWPDQTAVSSEVTKALASLVDQTAETKRNMYESKGSSAVADDSKLRPVIHCRAGVGRTAQLIGAMCMNDSRNSQLSVEDMVSQMRVQRNGIMVQKDEQLDVLIKLAEGQGRPLLNS

来源 Source

来源生物 organism	Yersinia pestis
NCBI 分类编号 ncbi_taxonomy_id	632
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

描述 description	ASP-ALA-ASP-GLU-FTY-LEU-NH2
分子量 formula_weight	836.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C,D,E,F

DADEYLX

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	603

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6. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1qz0a_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.45 — (Phosphotyrosine protein) phosphatases II
超家族 Superfamily superfamily	c.45.1 — (Phosphotyrosine protein) phosphatases II
家族 Family family	c.45.1.2 — Higher-molecular-weight phosphotyrosine protein phosphatases

结构域编号 domain_id	d1qz0b_
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.45 — (Phosphotyrosine protein) phosphatases II
超家族 Superfamily superfamily	c.45.1 — (Phosphotyrosine protein) phosphatases II
家族 Family family	c.45.1.2 — Higher-molecular-weight phosphotyrosine protein phosphatases

CATH v4.4 (2 domains)

结构域编号 domain_id	1qz0A00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	190 — Protein-Tyrosine Phosphatase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Protein tyrosine phosphatase superfamily

结构域编号 domain_id	1qz0B00
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	190 — Protein-Tyrosine Phosphatase; Chain A
同源超家族 H-superfamily homologous superfamily	10 — Protein tyrosine phosphatase superfamily

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7. 引用文献 (1)

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晶胞边长 a length_a	47.292 Å
晶胞边长 b length_b	53.450 Å
晶胞边长 c length_c	69.066 Å
晶胞夹角 α angle_alpha	109.61 °
晶胞夹角 β angle_beta	104.75 °
晶胞夹角 γ angle_gamma	89.98 °
晶胞分子数 Z z_pdb	4

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

分辨率 resolution	1.500 Å
最低分辨率 resolution_low	25.000 Å
R 因子 r_factor	—
R_work r_work	0.1880
R_free r_free	0.2090

fit	/app/data/saxs_computation/qz/1qz0/1qz0.fit
pddf	/app/data/pr_computation/qz/1qz0/1qz0.pr.out
profile	/app/data/saxs_computation/qz/1qz0/1qz0.dat

Crystal Structure of the Yersinia Pestis Phosphatase YopH in Complex with a Phosphotyrosyl Mimetic-Containing Hexapeptide

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

衍射实验 Diffraction

5. 实体与聚合体信息 (3)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

Entity 3 water

6. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)