2fzk

The Structure of Wild-Type E. Coli Aspartate Transcarbamoylase in Complex with Novel T State Inhibitors at 2.50 Resolution

Method: X-RAY DIFFRACTION D_max: 113.3 Å Quality: EXCELLENT

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	2fzk
沉积日期 deposition_date	2006-02-09
结构标题 title	The Structure of Wild-Type E. Coli Aspartate Transcarbamoylase in Complex with Novel T State Inhibitors at 2.50 Resolution
关键词 keywords	Inhibitors, allosteric transition, Xray structures, 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	37.47 Å
回转半径 Rg (电子) rg_electron	36.89 Å
零角强度 I(0) i0	172700000.00
分子量 molecular_weight	104450.0 kDa
排除体积 excluded_volume	130110 Å³
包络体积 envelope_volume	173210 Å³
水化壳体积 shell_volume	39550 Å³
包络直径 envelope_diameter	109.0 Å
壳层 Rg shell_rg	42.90 Å
包络 Rg envelope_rg	35.60 Å
形状 Rg shape_rg	36.90 Å
总 Rg total_rg	37.23 Å
总原子数 total_atoms	7326
残基数 n_residues	924
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	113.3 Å
Rg (实空间) rg_real	37.34 Å
Rg 误差 (实空间) rg_real_error	1.02 Å
I(0) (实空间) i0_real	1.7270e+08
I(0) 误差 (实空间) i0_real_error	2.9210e+06
Rg (倒空间) rg_reciprocal	37.43 Å
I(0) (倒空间) i0_reciprocal	172700000.0000
解质量估计 total_estimate	0.9004
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	3
主峰位置 r_peak_primary	62.0 Å
偏度 Skewness skewness	0.023
峰度 Kurtosis kurtosis	-0.907
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	20180000.0000
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: 0.925; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.943

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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	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	7855

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
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	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	3,5-BIS[(PHOSPHONOACETYL)AMINO]BENZOIC ACID
分子量 formula_weight	396.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 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 5 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 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	529

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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	d2fzka1
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	d2fzka2
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	d2fzkb1
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	d2fzkb2
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	d2fzkc1
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	d2fzkc2
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	d2fzkd1
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	d2fzkd2
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	2fzkA01
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	2fzkA02
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	2fzkB01
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	2fzkB02
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	2fzkC01
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	2fzkC02
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	2fzkD01
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	2fzkD02
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	120.900 Å
晶胞边长 b length_b	120.900 Å
晶胞边长 c length_c	141.610 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	28.450 Å
R 因子 r_factor	0.2110
R_work r_work	0.2110
R_free r_free	0.2389

fit	/app/data/saxs_computation/fz/2fzk/2fzk.fit
pddf	/app/data/pr_computation/fz/2fzk/2fzk.pr.out
profile	/app/data/saxs_computation/fz/2fzk/2fzk.dat

The Structure of Wild-Type E. Coli Aspartate Transcarbamoylase in Complex with Novel T State Inhibitors at 2.50 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

衍射实验 Diffraction

5. 实体与聚合体信息 (6)

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 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)