2ivg

SITE DIRECTED MUTAGENESIS OF KEY RESIDUES INVOLVED IN THE CATALYTIC MECHANISM OF CYANASE

Method: X-RAY DIFFRACTION D_max: 94.6 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	2ivg
沉积日期 deposition_date	2006-06-13
结构标题 title	SITE DIRECTED MUTAGENESIS OF KEY RESIDUES INVOLVED IN THE CATALYTIC MECHANISM OF CYANASE
关键词 keywords	MIDWEST CENTER FOR STRUCTURAL GENOMICS, PROTEIN STRUCTURE INITIATIVE, PSI, MCSG, LYASE, CYANATE DEGRADATION; LYASE
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	33.17 Å
回转半径 Rg (电子) rg_electron	32.00 Å
零角强度 I(0) i0	446469000.00
分子量 molecular_weight	172800.0 kDa
排除体积 excluded_volume	217610 Å³
包络体积 envelope_volume	255360 Å³
水化壳体积 shell_volume	61170 Å³
包络直径 envelope_diameter	93.0 Å
壳层 Rg shell_rg	42.49 Å
包络 Rg envelope_rg	31.81 Å
形状 Rg shape_rg	31.99 Å
总 Rg total_rg	32.81 Å
总原子数 total_atoms	12079
残基数 n_residues	1560
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	94.6 Å
Rg (实空间) rg_real	32.81 Å
Rg 误差 (实空间) rg_real_error	0.35 Å
I(0) (实空间) i0_real	4.4650e+08
I(0) 误差 (实空间) i0_real_error	6.1490e+06
Rg (倒空间) rg_reciprocal	32.97 Å
I(0) (倒空间) i0_reciprocal	446500000.0000
解质量估计 total_estimate	0.8993
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	43.3 Å
偏度 Skewness skewness	0.001
峰度 Kurtosis kurtosis	-0.593
角度范围 angular_range	— – 0.2400 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	175600000.0000
实空间数据点数 n_real_points	49
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.962; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.959; Smooth: 0.841

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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 (5)

Entity 1 polymer

描述 description	CYANATE LYASE
分子量 formula_weight	17011.7 kDa
EC 编号 ec_number	4.2.1.104
突变 mutation	YES
来源方法 src_method	man
拷贝数 entity_count	10

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H,I,J
原子数 atom_count	13926

MIQSQINRNIRLDLADAILLSKAKKDLSFAEIADGTGLAEAFVTAALLGQQALPADAARLVGAKLDLDEDSILLLQMIPLRGCIDDRIPTDPTMYRFYEMLQVYGTTLKALVHEKFGDGIISAINFKLDVKKVADPEGGERAVITLDGKYGPTKPF

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	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	29

Entity 3 non-polymer

描述 description	CHLORIDE ION
分子量 formula_weight	35.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	20

Entity 4 non-polymer

描述 description	AZIDE ION
分子量 formula_weight	42.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 5 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	1754

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6. 折叠分类 (SCOP + CATH) 40 domains

SCOP 2.08 (20 domains)

结构域编号 domain_id	d2ivga1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.35 — lambda repressor-like DNA-binding domains
超家族 Superfamily superfamily	a.35.1 — lambda repressor-like DNA-binding domains
家族 Family family	a.35.1.4 — Cyanase N-terminal domain

结构域编号 domain_id	d2ivga2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.72 — Cyanase C-terminal domain
超家族 Superfamily superfamily	d.72.1 — Cyanase C-terminal domain
家族 Family family	d.72.1.1 — Cyanase C-terminal domain

结构域编号 domain_id	d2ivgb1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.35 — lambda repressor-like DNA-binding domains
超家族 Superfamily superfamily	a.35.1 — lambda repressor-like DNA-binding domains
家族 Family family	a.35.1.4 — Cyanase N-terminal domain

结构域编号 domain_id	d2ivgb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.72 — Cyanase C-terminal domain
超家族 Superfamily superfamily	d.72.1 — Cyanase C-terminal domain
家族 Family family	d.72.1.1 — Cyanase C-terminal domain

结构域编号 domain_id	d2ivgc1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.35 — lambda repressor-like DNA-binding domains
超家族 Superfamily superfamily	a.35.1 — lambda repressor-like DNA-binding domains
家族 Family family	a.35.1.4 — Cyanase N-terminal domain

结构域编号 domain_id	d2ivgc2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.72 — Cyanase C-terminal domain
超家族 Superfamily superfamily	d.72.1 — Cyanase C-terminal domain
家族 Family family	d.72.1.1 — Cyanase C-terminal domain

结构域编号 domain_id	d2ivgd1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.35 — lambda repressor-like DNA-binding domains
超家族 Superfamily superfamily	a.35.1 — lambda repressor-like DNA-binding domains
家族 Family family	a.35.1.4 — Cyanase N-terminal domain

结构域编号 domain_id	d2ivgd2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.72 — Cyanase C-terminal domain
超家族 Superfamily superfamily	d.72.1 — Cyanase C-terminal domain
家族 Family family	d.72.1.1 — Cyanase C-terminal domain

结构域编号 domain_id	d2ivge1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.35 — lambda repressor-like DNA-binding domains
超家族 Superfamily superfamily	a.35.1 — lambda repressor-like DNA-binding domains
家族 Family family	a.35.1.4 — Cyanase N-terminal domain

结构域编号 domain_id	d2ivge2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.72 — Cyanase C-terminal domain
超家族 Superfamily superfamily	d.72.1 — Cyanase C-terminal domain
家族 Family family	d.72.1.1 — Cyanase C-terminal domain

结构域编号 domain_id	d2ivgf1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.35 — lambda repressor-like DNA-binding domains
超家族 Superfamily superfamily	a.35.1 — lambda repressor-like DNA-binding domains
家族 Family family	a.35.1.4 — Cyanase N-terminal domain

结构域编号 domain_id	d2ivgf2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.72 — Cyanase C-terminal domain
超家族 Superfamily superfamily	d.72.1 — Cyanase C-terminal domain
家族 Family family	d.72.1.1 — Cyanase C-terminal domain

结构域编号 domain_id	d2ivgg1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.35 — lambda repressor-like DNA-binding domains
超家族 Superfamily superfamily	a.35.1 — lambda repressor-like DNA-binding domains
家族 Family family	a.35.1.4 — Cyanase N-terminal domain

结构域编号 domain_id	d2ivgg2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.72 — Cyanase C-terminal domain
超家族 Superfamily superfamily	d.72.1 — Cyanase C-terminal domain
家族 Family family	d.72.1.1 — Cyanase C-terminal domain

结构域编号 domain_id	d2ivgh1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.35 — lambda repressor-like DNA-binding domains
超家族 Superfamily superfamily	a.35.1 — lambda repressor-like DNA-binding domains
家族 Family family	a.35.1.4 — Cyanase N-terminal domain

结构域编号 domain_id	d2ivgh2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.72 — Cyanase C-terminal domain
超家族 Superfamily superfamily	d.72.1 — Cyanase C-terminal domain
家族 Family family	d.72.1.1 — Cyanase C-terminal domain

结构域编号 domain_id	d2ivgi1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.35 — lambda repressor-like DNA-binding domains
超家族 Superfamily superfamily	a.35.1 — lambda repressor-like DNA-binding domains
家族 Family family	a.35.1.4 — Cyanase N-terminal domain

结构域编号 domain_id	d2ivgi2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.72 — Cyanase C-terminal domain
超家族 Superfamily superfamily	d.72.1 — Cyanase C-terminal domain
家族 Family family	d.72.1.1 — Cyanase C-terminal domain

结构域编号 domain_id	d2ivgj1
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.35 — lambda repressor-like DNA-binding domains
超家族 Superfamily superfamily	a.35.1 — lambda repressor-like DNA-binding domains
家族 Family family	a.35.1.4 — Cyanase N-terminal domain

结构域编号 domain_id	d2ivgj2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.72 — Cyanase C-terminal domain
超家族 Superfamily superfamily	d.72.1 — Cyanase C-terminal domain
家族 Family family	d.72.1.1 — Cyanase C-terminal domain

CATH v4.4 (20 domains)

结构域编号 domain_id	2ivgA01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	260 — 434 Repressor (Amino-terminal Domain)
同源超家族 H-superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

结构域编号 domain_id	2ivgA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1160 — Cyanate Lyase; Chain: A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Cyanate lyase, C-terminal domain

结构域编号 domain_id	2ivgB01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	260 — 434 Repressor (Amino-terminal Domain)
同源超家族 H-superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

结构域编号 domain_id	2ivgB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1160 — Cyanate Lyase; Chain: A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Cyanate lyase, C-terminal domain

结构域编号 domain_id	2ivgC01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	260 — 434 Repressor (Amino-terminal Domain)
同源超家族 H-superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

结构域编号 domain_id	2ivgC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1160 — Cyanate Lyase; Chain: A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Cyanate lyase, C-terminal domain

结构域编号 domain_id	2ivgD01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	260 — 434 Repressor (Amino-terminal Domain)
同源超家族 H-superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

结构域编号 domain_id	2ivgD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1160 — Cyanate Lyase; Chain: A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Cyanate lyase, C-terminal domain

结构域编号 domain_id	2ivgE01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	260 — 434 Repressor (Amino-terminal Domain)
同源超家族 H-superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

结构域编号 domain_id	2ivgE02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1160 — Cyanate Lyase; Chain: A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Cyanate lyase, C-terminal domain

结构域编号 domain_id	2ivgF01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	260 — 434 Repressor (Amino-terminal Domain)
同源超家族 H-superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

结构域编号 domain_id	2ivgF02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1160 — Cyanate Lyase; Chain: A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Cyanate lyase, C-terminal domain

结构域编号 domain_id	2ivgG01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	260 — 434 Repressor (Amino-terminal Domain)
同源超家族 H-superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

结构域编号 domain_id	2ivgG02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1160 — Cyanate Lyase; Chain: A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Cyanate lyase, C-terminal domain

结构域编号 domain_id	2ivgH01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	260 — 434 Repressor (Amino-terminal Domain)
同源超家族 H-superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

结构域编号 domain_id	2ivgH02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1160 — Cyanate Lyase; Chain: A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Cyanate lyase, C-terminal domain

结构域编号 domain_id	2ivgI01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	260 — 434 Repressor (Amino-terminal Domain)
同源超家族 H-superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

结构域编号 domain_id	2ivgI02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1160 — Cyanate Lyase; Chain: A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Cyanate lyase, C-terminal domain

结构域编号 domain_id	2ivgJ01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	260 — 434 Repressor (Amino-terminal Domain)
同源超家族 H-superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

结构域编号 domain_id	2ivgJ02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	1160 — Cyanate Lyase; Chain: A, domain 2
同源超家族 H-superfamily homologous superfamily	10 — Cyanate lyase, C-terminal domain

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7. 引用文献 (2)

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晶胞边长 a length_a	78.392 Å
晶胞边长 b length_b	80.897 Å
晶胞边长 c length_c	81.094 Å
晶胞夹角 α angle_alpha	70.69 °
晶胞夹角 β angle_beta	75.98 °
晶胞夹角 γ angle_gamma	65.15 °
晶胞分子数 Z z_pdb	10

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

分辨率 resolution	1.870 Å
最低分辨率 resolution_low	76.700 Å
R 因子 r_factor	0.1470
R_work r_work	0.1450
R_free r_free	0.1880