SAXSdb — 1duv

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1duv
沉积日期 deposition_date	2000-01-18
结构标题 title	;CRYSTAL STRUCTURE OF E. COLI ORNITHINE TRANSCARBAMOYLASE COMPLEXED WITH NDELTA-L-ORNITHINE-DIAMINOPHOSPHINYL-N-SULPHONIC ACID (PSORN) ;
关键词 keywords	ENZYME-INHIBITOR COMPLEX, 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	30.93 Å
回转半径 Rg (电子) rg_electron	30.16 Å
零角强度 I(0) i0	191982000.00
分子量 molecular_weight	109830.0 kDa
排除体积 excluded_volume	136960 Å³
包络体积 envelope_volume	158280 Å³
水化壳体积 shell_volume	42775 Å³
包络直径 envelope_diameter	95.1 Å
壳层 Rg shell_rg	38.26 Å
包络 Rg envelope_rg	30.18 Å
形状 Rg shape_rg	30.17 Å
总 Rg total_rg	30.76 Å
总原子数 total_atoms	7707
残基数 n_residues	999
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	95.9 Å
Rg (实空间) rg_real	30.80 Å
Rg 误差 (实空间) rg_real_error	0.59 Å
I(0) (实空间) i0_real	1.9200e+08
I(0) 误差 (实空间) i0_real_error	2.6740e+06
Rg (倒空间) rg_reciprocal	30.86 Å
I(0) (倒空间) i0_reciprocal	192000000.0000
解质量估计 total_estimate	0.9089
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	35.7 Å
偏度 Skewness skewness	0.158
峰度 Kurtosis kurtosis	-0.654
角度范围 angular_range	— – 0.2550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	148800000.0000
实空间数据点数 n_real_points	52
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.951; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.958

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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	ORNITHINE TRANSCARBAMOYLASE
分子量 formula_weight	36818.8 kDa
EC 编号 ec_number	2.1.3.3
来源方法 src_method	man
拷贝数 entity_count	3

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	G,H,I
原子数 atom_count	8442

SGFYHKHFLKLLDFTPAELNSLLQLAAKLKADKKSGKEEAKLTGKNIALIFEKDSTRTRCSFEVAAYDQGARVTYLGPSGSQIGHKESIKDTARVLGRMYDGIQYRGYGQEIVETLAEYASVPVWNGLTNEFHPTQLLADLLTMQEHLPGKAFNEMTLVYAGDARNNMGNSMLEAAALTGLDLRLVAPQACWPEAALVTECRALAQQNGGNITLTEDVAKGVEGADFIYTDVWVSMGEAKEKWAERIALLREYQVNSKMMQLTGNPEVKFLHCLPAFHDDQTTLGKKMAEEFGLHGGMEVTDEVFESAASIVFDQAENRMHTIKAVMVATLSK

来源 Source

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

Entity 2 non-polymer

描述 description	NDELTA-(N'-SULPHODIAMINOPHOSPHINYL)-L-ORNITHINE
分子量 formula_weight	290.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 3 non-polymer

描述 description	(4S)-2-METHYL-2,4-PENTANEDIOL
分子量 formula_weight	118.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	735

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6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1duvg1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.78 — ATC-like
超家族 Superfamily superfamily	c.78.1 — Aspartate/ornithine carbamoyltransferase
家族 Family family	c.78.1.1 — Aspartate/ornithine carbamoyltransferase

结构域编号 domain_id	d1duvg2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.78 — ATC-like
超家族 Superfamily superfamily	c.78.1 — Aspartate/ornithine carbamoyltransferase
家族 Family family	c.78.1.1 — Aspartate/ornithine carbamoyltransferase

结构域编号 domain_id	d1duvh1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.78 — ATC-like
超家族 Superfamily superfamily	c.78.1 — Aspartate/ornithine carbamoyltransferase
家族 Family family	c.78.1.1 — Aspartate/ornithine carbamoyltransferase

结构域编号 domain_id	d1duvh2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.78 — ATC-like
超家族 Superfamily superfamily	c.78.1 — Aspartate/ornithine carbamoyltransferase
家族 Family family	c.78.1.1 — Aspartate/ornithine carbamoyltransferase

结构域编号 domain_id	d1duvi1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.78 — ATC-like
超家族 Superfamily superfamily	c.78.1 — Aspartate/ornithine carbamoyltransferase
家族 Family family	c.78.1.1 — Aspartate/ornithine carbamoyltransferase

结构域编号 domain_id	d1duvi2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.78 — ATC-like
超家族 Superfamily superfamily	c.78.1 — Aspartate/ornithine carbamoyltransferase
家族 Family family	c.78.1.1 — Aspartate/ornithine carbamoyltransferase

CATH v4.4 (6 domains)

结构域编号 domain_id	1duvG01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1370 — Aspartate/ornithine carbamoyltransferase

结构域编号 domain_id	1duvG02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1370 — Aspartate/ornithine carbamoyltransferase

结构域编号 domain_id	1duvH01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1370 — Aspartate/ornithine carbamoyltransferase

结构域编号 domain_id	1duvH02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1370 — Aspartate/ornithine carbamoyltransferase

结构域编号 domain_id	1duvI01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1370 — Aspartate/ornithine carbamoyltransferase

结构域编号 domain_id	1duvI02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1370 — Aspartate/ornithine carbamoyltransferase

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7. 引用文献 (1)

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晶胞边长 a length_a	86.680 Å
晶胞边长 b length_b	134.230 Å
晶胞边长 c length_c	109.300 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	12

空间群 space_group	P 21 21 2
空间群编号 int_tables_number	18
晶系 crystal_system	—

分辨率 resolution	1.700 Å
最低分辨率 resolution_low	40.000 Å
R 因子 r_factor	0.1940
R_work r_work	0.1920
R_free r_free	0.2210

fit	/app/data/saxs_computation/du/1duv/1duv.fit
pddf	/app/data/pr_computation/du/1duv/1duv.pr.out
profile	/app/data/saxs_computation/du/1duv/1duv.dat

;CRYSTAL STRUCTURE OF E. COLI ORNITHINE TRANSCARBAMOYLASE COMPLEXED WITH NDELTA-L-ORNITHINE-DIAMINOPHOSPHINYL-N-SULPHONIC ACID (PSORN) ;

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