SAXSdb — 1kcx

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1kcx
沉积日期 deposition_date	2001-11-11
结构标题 title	X-ray structure of NYSGRC target T-45
关键词 keywords	;alpha/beta barrel, Structural Genomics, PSI, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, NYSGXRC, SIGNALING PROTEIN ;; SIGNALING PROTEIN
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	30.09 Å
回转半径 Rg (电子) rg_electron	29.18 Å
零角强度 I(0) i0	167439000.00
分子量 molecular_weight	103470.0 kDa
排除体积 excluded_volume	129800 Å³
包络体积 envelope_volume	152140 Å³
水化壳体积 shell_volume	42261 Å³
包络直径 envelope_diameter	96.9 Å
壳层 Rg shell_rg	37.43 Å
包络 Rg envelope_rg	29.30 Å
形状 Rg shape_rg	29.19 Å
总 Rg total_rg	29.91 Å
总原子数 total_atoms	7282
残基数 n_residues	952
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	94.0 Å
Rg (实空间) rg_real	30.01 Å
Rg 误差 (实空间) rg_real_error	0.47 Å
I(0) (实空间) i0_real	1.6740e+08
I(0) 误差 (实空间) i0_real_error	2.3850e+06
Rg (倒空间) rg_reciprocal	30.04 Å
I(0) (倒空间) i0_reciprocal	167400000.0000
解质量估计 total_estimate	0.9044
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	35.5 Å
偏度 Skewness skewness	0.260
峰度 Kurtosis kurtosis	-0.520
角度范围 angular_range	— – 0.2650 Å⁻¹
当前正则化参数 α current_alpha	0.0001
最高正则化参数 α highest_alpha	66030000.0000
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: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.954

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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 (2)

Entity 1 polymer

描述 description	DIHYDROPYRIMIDINASE RELATED PROTEIN-1
分子量 formula_weight	56372.0 kDa
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	8086

SIPHITSDRLLIRGGRIINDDQSFYADVYLEDGLIKQIGENLIVPGGVKTIEANGRMVIPGGIDVNTYLQKPSQGMTSADDFFQGTKAALAGGTTMIIDHVVPEPGSSLLTSFEKWHEAADTKSCCDYSLHVDITSWYDGVREELEVLVQDKGVNSFQVYMAYKDLYQMSDSQLYEAFTFLKGLGAVILVHAENGDLIAQEQKRILEMGITGPEGHALSRPEELEAEAVFRAIAIAGRINCPVYITKVMSKSAADIIALARKKGPLVFGEPIAASLGTDGTHYWSKNWAKAAAFVTSPPLSPDPTTPDYLTSLLACGDLQVTGSGHCPYSTAQKAVGKDNFTLIPEGVNGIEERMTVVWDKAVATGKMDENQFVAVTSTNAAKIFNLYPRKGRIAVGSDADVVIWDPDKMKTITAKSHKSTVEYNIFEGMECHGSPLVVISQGKIVFEDGNISVSKGMGRFIPRKPFPEHLYQRVRIRSKVFGLHSVSRGMYDGPVYEVPATPKHAAPAPSAKSSPSK

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI 分类编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 2 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	804

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1kcxa1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.92 — Composite domain of metallo-dependent hydrolases
超家族 Superfamily superfamily	b.92.1 — Composite domain of metallo-dependent hydrolases
家族 Family family	b.92.1.3 — Hydantoinase (dihydropyrimidinase)

结构域编号 domain_id	d1kcxa2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.9 — Metallo-dependent hydrolases
家族 Family family	c.1.9.6 — Hydantoinase (dihydropyrimidinase), catalytic domain

结构域编号 domain_id	d1kcxb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.92 — Composite domain of metallo-dependent hydrolases
超家族 Superfamily superfamily	b.92.1 — Composite domain of metallo-dependent hydrolases
家族 Family family	b.92.1.3 — Hydantoinase (dihydropyrimidinase)

结构域编号 domain_id	d1kcxb2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.9 — Metallo-dependent hydrolases
家族 Family family	c.1.9.6 — Hydantoinase (dihydropyrimidinase), catalytic domain

CATH v4.4 (4 domains)

结构域编号 domain_id	1kcxA01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	40 — Urease, subunit C; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Urease, subunit C, domain 1

结构域编号 domain_id	1kcxA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	140 — Metal-dependent hydrolases

结构域编号 domain_id	1kcxB01
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	40 — Urease, subunit C; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Urease, subunit C, domain 1

结构域编号 domain_id	1kcxB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	140 — Metal-dependent hydrolases

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7. 引用文献 (1)

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晶胞边长 a length_a	123.396 Å
晶胞边长 b length_b	152.111 Å
晶胞边长 c length_c	157.165 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	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	2.120 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	0.2330

fit	/app/data/saxs_computation/kc/1kcx/1kcx.fit
pddf	/app/data/pr_computation/kc/1kcx/1kcx.pr.out
profile	/app/data/saxs_computation/kc/1kcx/1kcx.dat

X-ray structure of NYSGRC target T-45

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