1za2

Structure of wild-type E. coli Aspartate Transcarbamoylase in the presence of CTP, carbamoyl phosphate at 2.50 A resolution

Method: X-RAY DIFFRACTION D_max: 108.2 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	1za2
沉积日期 deposition_date	2005-04-05
结构标题 title	Structure of wild-type E. coli Aspartate Transcarbamoylase in the presence of CTP, carbamoyl phosphate at 2.50 A resolution
关键词 keywords	ordered substrate binding, cooperativity, 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	37.34 Å
回转半径 Rg (电子) rg_electron	36.77 Å
零角强度 I(0) i0	166197000.00
分子量 molecular_weight	102370.0 kDa
排除体积 excluded_volume	127510 Å³
包络体积 envelope_volume	169710 Å³
水化壳体积 shell_volume	38793 Å³
包络直径 envelope_diameter	108.6 Å
壳层 Rg shell_rg	42.93 Å
包络 Rg envelope_rg	35.43 Å
形状 Rg shape_rg	36.79 Å
总 Rg total_rg	37.11 Å
总原子数 total_atoms	7177
残基数 n_residues	908
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	108.2 Å
Rg (实空间) rg_real	37.22 Å
Rg 误差 (实空间) rg_real_error	0.88 Å
I(0) (实空间) i0_real	1.6620e+08
I(0) 误差 (实空间) i0_real_error	3.0940e+06
Rg (倒空间) rg_reciprocal	37.30 Å
I(0) (倒空间) i0_reciprocal	166200000.0000
解质量估计 total_estimate	0.8567
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	61.9 Å
偏度 Skewness skewness	0.033
峰度 Kurtosis kurtosis	-0.896
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	18060000.0000
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: 0.968; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.258

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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 (7)

Entity 1 polymer

描述 description	Aspartate carbamoyltransferase catalytic chain
分子量 formula_weight	34337.1 kDa
EC 编号 ec_number	2.1.3.2
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,C
原子数 atom_count	7558

ANPLYQKHIISINDLSRDDLNLVLATAAKLKANPQPELLKHKVIASCFFEASTRTRLSFETSMHRLGASVVGFSDSANTSLGKKGETLADTISVISTYVDAIVMRHPQEGAARLATEFSGNVPVLNAGDGSNQHPTQTLLDLFTIQETQGRLDNLHVAMVGDLKYGRTVHSLTQALAKFDGNRFYFIAPDALAMPQYILDMLDEKGIAWSLHSSIEEVMAEVDILYMTRVQKERLDPSEYANVKAQFVLRASDLHNAKANMKVLHPLPRVDEIATDVDKTPHAWYFQQAGNGIFARQALLALVLNRDLVL

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 polymer

描述 description	Aspartate carbamoyltransferase regulatory chain
分子量 formula_weight	17143.6 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	B,D

MTHDNKLQVEAIKRGTVIDHIPAQIGFKLLSLFKLTETDQRITIGLNLPSGEMGRKDLIKIENTFLSEDQVDQLALYAPQATVNRIDNYEVVGKSRPSLPERIDNVLVCPNSNCISHAEPVSSSFAVRKRANDIALKCKYCEKEFSHNVVLAN

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 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	1

Entity 4 non-polymer

描述 description	PHOSPHORIC ACID MONO(FORMAMIDE)ESTER
分子量 formula_weight	141.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 5 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 6 non-polymer

描述 description	CYTIDINE-5'-TRIPHOSPHATE
分子量 formula_weight	483.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 7 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	381

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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	d1za2a1
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	d1za2a2
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	d1za2b1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.2 — Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
家族 Family family	d.58.2.1 — Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain

结构域编号 domain_id	d1za2b2
类 Class class	g — Small proteins
折叠类型 Fold fold	g.41 — Rubredoxin-like
超家族 Superfamily superfamily	g.41.7 — Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain
家族 Family family	g.41.7.1 — Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain

结构域编号 domain_id	d1za2c1
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	d1za2c2
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	d1za2d1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.58 — Ferredoxin-like
超家族 Superfamily superfamily	d.58.2 — Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
家族 Family family	d.58.2.1 — Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain

结构域编号 domain_id	d1za2d2
类 Class class	g — Small proteins
折叠类型 Fold fold	g.41 — Rubredoxin-like
超家族 Superfamily superfamily	g.41.7 — Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain
家族 Family family	g.41.7.1 — Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain

CATH v4.4 (8 domains)

结构域编号 domain_id	1za2A01
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	1za2A02
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	1za2B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	140 — Aspartate carbamoyltransferase regulatory subunit, N-terminal domain

结构域编号 domain_id	1za2B02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	20 — Aspartate carbamoyltransferase regulatory subunit, C-terminal domain

结构域编号 domain_id	1za2C01
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	1za2C02
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	1za2D01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	70 — Alpha-Beta Plaits
同源超家族 H-superfamily homologous superfamily	140 — Aspartate carbamoyltransferase regulatory subunit, N-terminal domain

结构域编号 domain_id	1za2D02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	30 — Roll
拓扑 Topology topology	30 — SH3 type barrels.
同源超家族 H-superfamily homologous superfamily	20 — Aspartate carbamoyltransferase regulatory subunit, C-terminal domain

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7. 引用文献 (1)

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晶胞边长 a length_a	121.442 Å
晶胞边长 b length_b	121.442 Å
晶胞边长 c length_c	142.547 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	120.00 °
晶胞分子数 Z z_pdb	12

空间群 space_group	P 3 2 1
空间群编号 int_tables_number	150
晶系 crystal_system	—

分辨率 resolution	2.500 Å
最低分辨率 resolution_low	30.000 Å
R 因子 r_factor	0.1970
R_work r_work	0.1970
R_free r_free	0.2510

fit	/app/data/saxs_computation/za/1za2/1za2.fit
pddf	/app/data/pr_computation/za/1za2/1za2.pr.out
profile	/app/data/saxs_computation/za/1za2/1za2.dat

Structure of wild-type E. coli Aspartate Transcarbamoylase in the presence of CTP, carbamoyl phosphate at 2.50 A resolution

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 (7)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 polymer

聚合体 Polymer

来源 Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 water

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)