SAXSdb — 2hke

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	2hke
沉积日期 deposition_date	2006-07-04
结构标题 title	Mevalonate diphosphate decarboxylase from Trypanosoma brucei
关键词 keywords	mevalonate diphosphate decarboxylase, diphosphomevalonate decarboxylase, decarboxylase, 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	31.59 Å
回转半径 Rg (电子) rg_electron	31.32 Å
零角强度 I(0) i0	110255000.00
分子量 molecular_weight	83569.0 kDa
排除体积 excluded_volume	104760 Å³
包络体积 envelope_volume	128550 Å³
水化壳体积 shell_volume	35735 Å³
包络直径 envelope_diameter	121.4 Å
壳层 Rg shell_rg	36.34 Å
包络 Rg envelope_rg	31.57 Å
形状 Rg shape_rg	31.30 Å
总 Rg total_rg	31.80 Å
总原子数 total_atoms	5843
残基数 n_residues	753
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	115.3 Å
Rg (实空间) rg_real	31.88 Å
Rg 误差 (实空间) rg_real_error	1.22 Å
I(0) (实空间) i0_real	1.1030e+08
I(0) 误差 (实空间) i0_real_error	1.8770e+06
Rg (倒空间) rg_reciprocal	31.76 Å
I(0) (倒空间) i0_reciprocal	110200000.0000
解质量估计 total_estimate	0.6316
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	32.3 Å
偏度 Skewness skewness	0.607
峰度 Kurtosis kurtosis	0.027
角度范围 angular_range	— – 0.2500 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	24370000.0000
实空间数据点数 n_real_points	51
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.640; Stabil: 1.000; Sysdev: 0.169; Positv: 1.000; Valcen: 0.837; Smooth: 0.942

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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 (3)

Entity 1 polymer

描述 description	Diphosphomevalonate decarboxylase, putative
分子量 formula_weight	41945.3 kDa
EC 编号 ec_number	4.1.1.33
突变 mutation	D92E
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,B
原子数 atom_count	6562

MSDQCVTVEAPINIAFIKYWGKREGGETLILPTNDSFSITLSASPFRSKTSVELRDDIETDTLRLNGTEVDVGKTPRVQSMLLHLRSTCPEELKNKKVNIVSENNFPTAAGMASSASGYCAMSAALIRAFKSTTNVSMLARLGSGSACRSAFGGFVIWNKGEKPDGSDCVATQFVDETHWPEIQVMCAVLKGAQKDVSSTKGMQQSLKTSPLMKKRISETVPERMKIASRAIKARDFATFAEIAMLESDDLQEICATTEPKITYATEDSYAMIRLVKAYNAKKGRTALAYTFDAGANCFLFVLKEDLPEAVAMLMEHFPTPFEKFFFGDRELLEKVKVVSLPDEYKKLIDHPKKPFEMLLQSPVGCGVKYLGPSESLIPP

来源 Source

来源生物 organism	Trypanosoma brucei
NCBI 分类编号 ncbi_taxonomy_id	5691
宿主生物 host_organism	Escherichia coli BL21(DE3)

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	6

Entity 3 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	712

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6. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d2hkea1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.14 — Ribosomal protein S5 domain 2-like
超家族 Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
家族 Family family	d.14.1.0 — automated matches

结构域编号 domain_id	d2hkea2
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.58.26 — GHMP Kinase, C-terminal domain
家族 Family family	d.58.26.0 — automated matches

结构域编号 domain_id	d2hkeb1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.14 — Ribosomal protein S5 domain 2-like
超家族 Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
家族 Family family	d.14.1.0 — automated matches

结构域编号 domain_id	d2hkeb2
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.58.26 — GHMP Kinase, C-terminal domain
家族 Family family	d.58.26.0 — automated matches

CATH v4.4 (4 domains)

结构域编号 domain_id	2hkeA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	230 — Ribosomal Protein S5; domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	2hkeA02
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	890 — GHMP kinase, C-terminal domain

结构域编号 domain_id	2hkeB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	230 — Ribosomal Protein S5; domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	2hkeB02
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	890 — GHMP kinase, C-terminal domain

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7. 引用文献 (2)

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晶胞边长 a length_a	51.463 Å
晶胞边长 b length_b	168.666 Å
晶胞边长 c length_c	54.850 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	118.78 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	1.800 Å
最低分辨率 resolution_low	42.180 Å
R 因子 r_factor	0.1680
R_work r_work	0.1660
R_free r_free	0.2080

fit	/app/data/saxs_computation/hk/2hke/2hke.fit
pddf	/app/data/pr_computation/hk/2hke/2hke.pr.out
profile	/app/data/saxs_computation/hk/2hke/2hke.dat

Mevalonate diphosphate decarboxylase from Trypanosoma brucei

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