2dw6

Crystal structure of the mutant K184A of D-Tartrate Dehydratase from Bradyrhizobium japonicum complexed with Mg++ and D-tartrate

Method: X-RAY DIFFRACTION D_max: 110.5 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	2dw6
沉积日期 deposition_date	2006-08-07
结构标题 title	Crystal structure of the mutant K184A of D-Tartrate Dehydratase from Bradyrhizobium japonicum complexed with Mg++ and D-tartrate
关键词 keywords	D-Tartrate Dehydratase, Enolase superfamily, D-tartrate, L-tartrate, LYASE; 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	35.62 Å
回转半径 Rg (电子) rg_electron	35.01 Å
零角强度 I(0) i0	453495000.00
分子量 molecular_weight	172160.0 kDa
排除体积 excluded_volume	214880 Å³
包络体积 envelope_volume	259190 Å³
水化壳体积 shell_volume	58970 Å³
包络直径 envelope_diameter	115.5 Å
壳层 Rg shell_rg	43.83 Å
包络 Rg envelope_rg	34.95 Å
形状 Rg shape_rg	34.96 Å
总 Rg total_rg	35.69 Å
总原子数 total_atoms	12116
残基数 n_residues	1552
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	110.5 Å
Rg (实空间) rg_real	35.45 Å
Rg 误差 (实空间) rg_real_error	0.66 Å
I(0) (实空间) i0_real	4.5350e+08
I(0) 误差 (实空间) i0_real_error	7.2140e+06
Rg (倒空间) rg_reciprocal	35.56 Å
I(0) (倒空间) i0_reciprocal	453500000.0000
解质量估计 total_estimate	0.9034
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	45.2 Å
偏度 Skewness skewness	0.155
峰度 Kurtosis kurtosis	-0.537
角度范围 angular_range	— – 0.2200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	241500000.0000
实空间数据点数 n_real_points	45
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.941; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.924

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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	Bll6730 protein
分子量 formula_weight	43053.0 kDa
EC 编号 ec_number	4.2.1.81
突变 mutation	K184A
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	12582

MSVRIVDVREITKPISSPIRNAYIDFTKMTTSLVAVVTDVVREGKRVVGYGFNSNGRYGQGGLIRERFASRILEADPKKLLNEAGDNLDPDKVWAAMMINEKPGGHGERSVAVGTIDMAVWDAVAKIAGKPLFRLLAERHGVKANPRVFVYAAGGYYYPGKGLSMLRGEMRGYLDRGYNVVKMAIGGAPIEEDRMRIEAVLEEIGKDAQLAVDANGRFNLETGIAYAKMLRDYPLFWYEEVGDPLDYALQAALAEFYPGPMATGENLFSHQDARNLLRYGGMRPDRDWLQFDCALSYGLCEYQRTLEVLKTHGWSPSRCIPHGGHQMSLNIAAGLGLGGNESYPDLFQPYGGFPDGVRVENGHITMPDLPGIGFEGKSDLYKEMKALAE

来源 Source

来源生物 organism	Bradyrhizobium japonicum
NCBI 分类编号 ncbi_taxonomy_id	375
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	MAGNESIUM ION
分子量 formula_weight	24.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	D(-)-TARTARIC ACID
分子量 formula_weight	150.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 4 non-polymer

描述 description	L(+)-TARTARIC ACID
分子量 formula_weight	150.1 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	466

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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	d2dw6a1
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.1.11 — Enolase C-terminal domain-like
家族 Family family	c.1.11.2 — D-glucarate dehydratase-like

结构域编号 domain_id	d2dw6a2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.54 — Enolase N-terminal domain-like
超家族 Superfamily superfamily	d.54.1 — Enolase N-terminal domain-like
家族 Family family	d.54.1.0 — automated matches

结构域编号 domain_id	d2dw6b1
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.1.11 — Enolase C-terminal domain-like
家族 Family family	c.1.11.2 — D-glucarate dehydratase-like

结构域编号 domain_id	d2dw6b2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.54 — Enolase N-terminal domain-like
超家族 Superfamily superfamily	d.54.1 — Enolase N-terminal domain-like
家族 Family family	d.54.1.0 — automated matches

结构域编号 domain_id	d2dw6c1
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.1.11 — Enolase C-terminal domain-like
家族 Family family	c.1.11.2 — D-glucarate dehydratase-like

结构域编号 domain_id	d2dw6c2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.54 — Enolase N-terminal domain-like
超家族 Superfamily superfamily	d.54.1 — Enolase N-terminal domain-like
家族 Family family	d.54.1.0 — automated matches

结构域编号 domain_id	d2dw6d1
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.1.11 — Enolase C-terminal domain-like
家族 Family family	c.1.11.2 — D-glucarate dehydratase-like

结构域编号 domain_id	d2dw6d2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.54 — Enolase N-terminal domain-like
超家族 Superfamily superfamily	d.54.1 — Enolase N-terminal domain-like
家族 Family family	d.54.1.0 — automated matches

CATH v4.4 (8 domains)

结构域编号 domain_id	2dw6A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	390 — Enolase-like; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Enolase-like, N-terminal domain

结构域编号 domain_id	2dw6A02
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	120 — Enolase-like C-terminal domain

结构域编号 domain_id	2dw6B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	390 — Enolase-like; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Enolase-like, N-terminal domain

结构域编号 domain_id	2dw6B02
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	120 — Enolase-like C-terminal domain

结构域编号 domain_id	2dw6C01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	390 — Enolase-like; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Enolase-like, N-terminal domain

结构域编号 domain_id	2dw6C02
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	120 — Enolase-like C-terminal domain

结构域编号 domain_id	2dw6D01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	390 — Enolase-like; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Enolase-like, N-terminal domain

结构域编号 domain_id	2dw6D02
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	120 — Enolase-like C-terminal domain

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7. 引用文献 (1)

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晶胞边长 a length_a	150.997 Å
晶胞边长 b length_b	150.997 Å
晶胞边长 c length_c	444.101 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	48

空间群 space_group	P 61 2 2
空间群编号 int_tables_number	178
晶系 crystal_system	—

分辨率 resolution	2.300 Å
最低分辨率 resolution_low	25.000 Å
R 因子 r_factor	0.2110
R_work r_work	0.2090
R_free r_free	0.2320

fit	/app/data/saxs_computation/dw/2dw6/2dw6.fit
pddf	/app/data/pr_computation/dw/2dw6/2dw6.pr.out
profile	/app/data/saxs_computation/dw/2dw6/2dw6.dat